obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 153)

Brought to you by: balhoff, cmungall, cooperl09, elserj, and 5 others

obo-svn-commit — sends mail for all commits to svn repository

You can subscribe to this list here.

2006	Jan	Feb	Mar	Apr	May	Jun	Jul (18)	Aug (33)	Sep (30)	Oct (27)	Nov (59)	Dec (30)
2007	Jan (67)	Feb (44)	Mar (70)	Apr (73)	May (119)	Jun (31)	Jul (92)	Aug (86)	Sep (76)	Oct (152)	Nov (156)	Dec (85)
2008	Jan (111)	Feb (121)	Mar (107)	Apr (102)	May (45)	Jun (65)	Jul (62)	Aug (133)	Sep (56)	Oct (56)	Nov (17)	Dec (15)
2009	Jan (10)	Feb (5)	Mar (10)	Apr (14)	May (49)	Jun (94)	Jul (67)	Aug (23)	Sep (9)	Oct (92)	Nov (26)	Dec (51)
2010	Jan (105)	Feb (83)	Mar (52)	Apr (59)	May (68)	Jun (71)	Jul (127)	Aug (49)	Sep (91)	Oct (27)	Nov (33)	Dec (26)
2011	Jan (26)	Feb (45)	Mar (26)	Apr (28)	May (17)	Jun (15)	Jul (45)	Aug (33)	Sep (50)	Oct (22)	Nov (10)	Dec (21)
2012	Jan (33)	Feb (24)	Mar (36)	Apr (60)	May (60)	Jun (43)	Jul (114)	Aug (19)	Sep (35)	Oct (24)	Nov (64)	Dec (12)
2013	Jan (54)	Feb (58)	Mar (51)	Apr (46)	May (21)	Jun (29)	Jul (25)	Aug (25)	Sep (13)	Oct (7)	Nov (14)	Dec (27)
2014	Jan (10)	Feb (7)	Mar (16)	Apr (14)	May (19)	Jun (8)	Jul (15)	Aug (11)	Sep (5)	Oct (11)	Nov (11)	Dec (4)
2015	Jan (52)	Feb (27)	Mar (22)	Apr (17)	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (2)	Oct	Nov (2)	Dec
2016	Jan (2)	Feb	Mar	Apr (2)	May (1)	Jun (1)	Jul (3)	Aug (2)	Sep (2)	Oct (2)	Nov (2)	Dec
2017	Jan	Feb	Mar (1)	Apr (1)	May (4)	Jun	Jul	Aug (1)	Sep (1)	Oct (2)	Nov	Dec (1)
2018	Jan	Feb	Mar (4)	Apr	May (2)	Jun (2)	Jul (2)	Aug (2)	Sep (1)	Oct (2)	Nov (1)	Dec
2019	Jan	Feb	Mar	Apr	May	Jun	Jul (2)	Aug	Sep	Oct	Nov	Dec (3)
2020	Jan	Feb	Mar	Apr	May (2)	Jun (3)	Jul	Aug	Sep (2)	Oct	Nov	Dec

Flat | Threaded

<< < 1 .. 151 152 153 154 155 .. 183 > >> (Page 153 of 183)

[Obo-svn-commit] SF.net SVN: obo: [853] phenote/trunk

From: <ba...@us...> - 2007-08-30 15:04:33

Revision: 853
          http://obo.svn.sourceforge.net/obo/?rev=853&view=rev
Author:   balhoff
Date:     2007-08-30 08:04:36 -0700 (Thu, 30 Aug 2007)

Log Message:
-----------
Added notes field to phenomap config.  Fixed warning in CharacterTemplateController.

Modified Paths:
--------------
    phenote/trunk/conf/phenomap.cfg
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java

Modified: phenote/trunk/conf/phenomap.cfg
===================================================================
--- phenote/trunk/conf/phenomap.cfg	2007-08-29 22:13:54 UTC (rev 852)
+++ phenote/trunk/conf/phenomap.cfg	2007-08-30 15:04:36 UTC (rev 853)
@@ -43,5 +43,6 @@
   <ns:field name="Compare To" datatag="Compar" enable="true" groups="default"/>
   <ns:field name="Textual Description" syntax-abbrev="Desc" enable="true" colwidth="150" groups="default"/>
   <ns:field name="Image URI" syntax-abbrev="URI" enable="true" colwidth="150" groups="default"/>
+  <ns:field name="Notes" syntax-abbrev="Notes" enable="true" colwidth="150" groups="default"/>
   
 </ns:phenote-configuration>
\ No newline at end of file

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-29 22:13:54 UTC (rev 852)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-30 15:04:36 UTC (rev 853)
@@ -236,7 +236,7 @@
   private TemplateChooser createTemplateChooserInstance(String className) {
     final String errorMessage = "Failed creating TemplateChooser";
     try {
-      Class adapterClass = Class.forName(className);
+      Class<?> adapterClass = Class.forName(className);
       Object chooser = adapterClass.newInstance();
       return (TemplateChooser)chooser;
     } catch (ClassNotFoundException e) {


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [852] phenote/trunk/conf/birn.cfg

From: <mg...@us...> - 2007-08-29 22:13:50

Revision: 852
          http://obo.svn.sourceforge.net/obo/?rev=852&view=rev
Author:   mgibson
Date:     2007-08-29 15:13:54 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
quick fix - put smart atlas fields at end of new birn.cfg
as tab delim data expects fields to be in same order
but this can be fixed in the tab delim adapter at some point

Modified Paths:
--------------
    phenote/trunk/conf/birn.cfg

Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg	2007-08-29 21:40:19 UTC (rev 851)
+++ phenote/trunk/conf/birn.cfg	2007-08-29 22:13:54 UTC (rev 852)
@@ -17,14 +17,6 @@
 
   <!-- for smart atlas -->
   <ns:field name="Image Name" datatag="imagename" enable="true" desc="Name of image"/>
-  <ns:field name="Image Source" datatag="imagesource" enable="true" desc="Source of image"/>
-  <ns:field name="Annot type" datatag="annotationtype" enable="true" desc="Point,line,area,entireimage"/>
-  <ns:field name="Regions" datatag="regions" enable="true" desc="comma delim list of regions, break into sep chars?"/>
-  <ns:field name="Coordinates" datatag="coordinates" enable="true" desc="coordinates of user selection of image"/>
-  <ns:field name="User Name" datatag="userName" enable="true" desc="should this be hidden?, read only"/>
-  <ns:field name="Timestamp" datatag="timestamp" enable="true" desc="read only, hidden?"/>
-  <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
-  <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
 
   <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor" colwidth="67"/>
   <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely" colwidth="96"/>
@@ -64,6 +56,15 @@
   <ns:field name="Compare To" datatag="Compar" enable="true" colwidth="112"/>
   <ns:field name="Description" datatag="Desc" enable="true" colwidth="189"/>
   <ns:field name="Comment" datatag="Comm" enable="true" colwidth="886"/>
+  <ns:field name="Image Source" datatag="imagesource" enable="true" desc="Source of image"/>
+  <ns:field name="Annot type" datatag="annotationtype" enable="true" desc="Point,line,area,entireimage"/>
+  <ns:field name="Regions" datatag="regions" enable="true" desc="comma delim list of regions, break into sep chars?"/>
+  <ns:field name="Coordinates" datatag="coordinates" enable="true" desc="coordinates of user selection of image"/>
+  <ns:field name="User Name" datatag="userName" enable="true" desc="should this be hidden?, read only"/>
+  <ns:field name="Timestamp" datatag="timestamp" enable="true" desc="read only, hidden?"/>
+  <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
+  <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
+
   <!--*********************** SETTINGS ****************************-->
   <ns:uvic-graph enable="false"/>
   <ns:term-history enable="false"/>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [851] phenote/trunk/conf/birn.cfg

From: <mg...@us...> - 2007-08-29 21:40:20

Revision: 851
          http://obo.svn.sourceforge.net/obo/?rev=851&view=rev
Author:   mgibson
Date:     2007-08-29 14:40:19 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
woops - file name for sao was wrong

Modified Paths:
--------------
    phenote/trunk/conf/birn.cfg

Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg	2007-08-29 21:17:47 UTC (rev 850)
+++ phenote/trunk/conf/birn.cfg	2007-08-29 21:40:19 UTC (rev 851)
@@ -31,7 +31,7 @@
 
   <ns:field name="Entity" datatag="E" min-completion-chars="4" enable="true" colwidth="150">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
+    <ns:ontology name="SAO" file="SAO.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
@@ -49,7 +49,7 @@
 
   <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" enable="true" colwidth="114">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
-    <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
+    <ns:ontology name="SAO" file="SAO.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [850] phenote/trunk/conf

From: <mg...@us...> - 2007-08-29 21:17:48

Revision: 850
          http://obo.svn.sourceforge.net/obo/?rev=850&view=rev
Author:   mgibson
Date:     2007-08-29 14:17:47 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
put min-completion-chars="4" into entity fields with lots of ontologies
or 3 or 2
changed some syntax-abbrev to new datatag

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg
    phenote/trunk/conf/demo.cfg
    phenote/trunk/conf/flybase.cfg
    phenote/trunk/conf/parameciumDB.cfg
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/conf/smart-atlas.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/birn2.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -23,7 +23,7 @@
   <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a
     mouse strain or some other identifying factor"/>
   <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
-  <ns:field name="Entity" datatag="E" enable="true">
+  <ns:field name="Entity" min-completion-chars="4" datatag="E" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
@@ -43,7 +43,7 @@
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <!--ns:ontology name="SAO" file="SAO.obo"/-->

Modified: phenote/trunk/conf/demo.cfg
===================================================================
--- phenote/trunk/conf/demo.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/demo.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -33,12 +33,12 @@
   "http://www.your-repository.com/your_obo_file.obo"), then this site 
   will be checked for updates -->
   
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
-  <ns:field name="Genotype" syntax-abbrev="GT" enable="true"/>
-  <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
+  <ns:field name="Pub" datatag="PUB" enable="true"/>
+  <ns:field name="Genotype" datatag="GT" enable="true"/>
+  <ns:field name="Genetic Context" datatag="GC" enable="true">
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="3" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
@@ -46,11 +46,11 @@
     <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+  <ns:field name="Quality" datatag="Q" enable="true">
     <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
     <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="3" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="fma_obo.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
@@ -58,16 +58,16 @@
     <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
     <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
   </ns:field>
-  <ns:field name="Time" syntax-abbrev="T" enable="true"/>
-  <ns:field name="Count" syntax-abbrev="C" enable="true"/>
-  <ns:field name="Unit" syntax-abbrev="U" enable="true">
+  <ns:field name="Time" datatag="T" enable="true"/>
+  <ns:field name="Count" datatag="C" enable="true"/>
+  <ns:field name="Unit" datatag="U" enable="true">
     <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
   </ns:field>
-  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
+  <ns:field name="Abnormal" datatag="Tag" enable="true">
     <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
   </ns:field>
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
-  <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
+  <ns:field name="Description" datatag="Desc" enable="true"/>
+  <ns:field name="Evidence" datatag="EC" enable="false">
     <ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo"/>
   </ns:field>
   <!-- ******************** REVISION HISTORY *********************** --> 

Modified: phenote/trunk/conf/flybase.cfg
===================================================================
--- phenote/trunk/conf/flybase.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/flybase.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -29,15 +29,15 @@
   
   <!-- ******************** FIELD DEFINITIONS *********************** --> 
 
-  <ns:field name="Pub" syntax-abbrev="PUB"/>                      
+  <ns:field name="Pub" datatag="PUB"/>                      
 
-  <ns:field name="Genotype" syntax-abbrev="GT" type="FREE_TEXT"/>
+  <ns:field name="Genotype" datatag="GT" type="FREE_TEXT"/>
 
-  <ns:field name="Genetic Context" syntax-abbrev="GC">
+  <ns:field name="Genetic Context" datatag="GC">
     <ns:ontology  file="context.obo"/>
   </ns:field>
 
-  <ns:field name="Entity" syntax-abbrev="E">
+  <ns:field name="Entity" datatag="E" min-completion-chars="3">
      <!-- postcomp relationship-ontology="relationship.obo" repos-subdir="OBO_REL"/ -->
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
@@ -47,19 +47,19 @@
      <ns:ontology name="SP" file="spatial.obo"/>
   </ns:field>
 
-  <ns:field name="Quality"  syntax-abbrev="Q">
+  <ns:field name="Quality"  datatag="Q">
     <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
   </ns:field>
 
-  <ns:field name="Absent" syntax-abbrev="Tag">
+  <ns:field name="Absent" datatag="AbsentTag">
     <ns:ontology file="quality.obo" slim="absent_slim" />
   </ns:field>
 
-  <ns:field name="Abnormal" syntax-abbrev="Tag">
+  <ns:field name="Abnormal" datatag="Tag">
     <ns:ontology file="quality.obo" slim="abnormal_slim" />
   </ns:field>
 
-  <ns:field name="Description" syntax-abbrev="Desc"/>
+  <ns:field name="Description" datatag="Desc"/>
 
   <!-- ******************** REVISION HISTORY *********************** --> 
   <!-- 05.24.2007 - Latest update changes relationship.obo to ro.obo;  

Modified: phenote/trunk/conf/parameciumDB.cfg
===================================================================
--- phenote/trunk/conf/parameciumDB.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/parameciumDB.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -31,7 +31,7 @@
  
   <ns:field name="Description" syntax-abbrev="Desc"/>
   
-  <ns:field name="Entity" syntax-abbrev="E">
+  <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="2">
     <ns:ontology name="Paramecium Anatomy" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/para.obo"/>
     <ns:ontology name="Paramecium Ontology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/paro.obo"/>
     <ns:ontology name="Gene Onotology" file="http://paramecium.cgm.cnrs-gif.fr/phenote/obo/go.obo"/>

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.rnc	2007-08-29 21:17:47 UTC (rev 850)
@@ -19,7 +19,8 @@
     autocomplete-settings,
     field*,
     group*,
-    data-input-servlet
+    data-input-servlet,
+    character-mode
   }
 
 ## specify how the master config interacts with local/cached config
@@ -71,6 +72,16 @@
   attribute obsolete { xsd:boolean }
 }
 
+## what implementation of CharacterI to use, CHARACTER or OBO_ANNOTATION
+character-mode = element character-mode {
+  ## type of character to use
+  attribute mode { "CHARACTER" | "OBO_ANNOTATION" },
+  ## if using OBO_ANNOTATION, then specify the java mapping class to use
+  ## full java class name, eg phenote.datamodel.BasicAnnotationMappingDriver
+  attribute mapping { xsd:string }
+}
+
+## this is pase and should be phased out
 obo-repository = element obo-repository { attribute url-dir {xsd:string} }
 
 field = 

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/phenote-config.xsd	2007-08-29 21:17:47 UTC (rev 850)
@@ -15,6 +15,7 @@
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:field"/>
         <xs:element minOccurs="0" maxOccurs="unbounded" ref="x:group"/>
         <xs:element ref="x:data-input-servlet"/>
+        <xs:element ref="x:character-mode"/>
       </xs:sequence>
       <xs:attribute name="version" use="required" type="xs:string"/>
       <xs:attribute name="description" use="required" type="xs:string"/>
@@ -74,6 +75,11 @@
       <xs:attribute name="obsolete" use="required" type="xs:boolean"/>
     </xs:complexType>
   </xs:element>
+  <xs:element name="character-mode">
+    <xs:complexType>
+      <xs:attribute name="mode" use="required" type="xs:string"/>
+    </xs:complexType>
+  </xs:element>
   <xs:element name="obo-repository">
     <xs:complexType>
       <xs:attribute name="url-dir" use="required" type="xs:string"/>

Modified: phenote/trunk/conf/smart-atlas.cfg
===================================================================
--- phenote/trunk/conf/smart-atlas.cfg	2007-08-29 21:02:47 UTC (rev 849)
+++ phenote/trunk/conf/smart-atlas.cfg	2007-08-29 21:17:47 UTC (rev 850)
@@ -30,7 +30,7 @@
   <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
   <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
 
-  <ns:field name="Entity" datatag="E" enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="4"  enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
@@ -52,7 +52,7 @@
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [849] phenote/trunk/conf/ncbo.cfg

From: <mg...@us...> - 2007-08-29 21:02:51

Revision: 849
          http://obo.svn.sourceforge.net/obo/?rev=849&view=rev
Author:   mgibson
Date:     2007-08-29 14:02:47 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
add minimum completion chars to ncbo.cfg for entity field
nicole feel free to take this out or change it
its set to 3 - which is kinda low

Modified Paths:
--------------
    phenote/trunk/conf/ncbo.cfg

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================
--- phenote/trunk/conf/ncbo.cfg	2007-08-29 18:42:13 UTC (rev 848)
+++ phenote/trunk/conf/ncbo.cfg	2007-08-29 21:02:47 UTC (rev 849)
@@ -40,7 +40,7 @@
     <ns:ontology name="Genetic Context" file="context.obo"/>
   </ns:field>
 
-  <ns:field name="Entity" datatag="E" enable="true">
+  <ns:field name="Entity" datatag="E" min-completion-chars="3" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>
@@ -56,7 +56,7 @@
     <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2" enable="true" desc="To be used when using relational qualities">
+  <ns:field name="Add'l Entity" datatag="E2"  min-completion-chars="3" enable="true" desc="To be used when using relational qualities">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [848] phenote/trunk/src/java/phenote/gui/field

From: <mg...@us...> - 2007-08-29 18:42:10

Revision: 848
          http://obo.svn.sourceforge.net/obo/?rev=848&view=rev
Author:   mgibson
Date:     2007-08-29 11:42:13 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
fixed bug with new completion optimization - 
completion terms were retaining state about previous matching 
even if it was no longer true - as in no longer starts with
thanks nicole for catching this

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
    phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java

Modified: phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-08-29 18:21:26 UTC (rev 847)
+++ phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-08-29 18:42:13 UTC (rev 848)
@@ -141,6 +141,7 @@
     // alternatively could just remove terms from prev list???
     SearchTermList newList = new SearchTermList();
     for (CompletionTerm ct : prevList) {
+      ct.resetMatchState(); // reusing ct has stale match state from previous search
       if (ct.matches(input,searchParams))
         newList.addTerm(ct);
     }

Modified: phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java	2007-08-29 18:21:26 UTC (rev 847)
+++ phenote/trunk/src/java/phenote/gui/field/CompletionTerm.java	2007-08-29 18:42:13 UTC (rev 848)
@@ -37,6 +37,15 @@
   boolean isExactMatch() { return exactMatch; }
   boolean isStartsWithMatch() { return startsWith; }
 
+  void resetMatchState() {
+    termMatch = false;
+    isSynMatch = false;
+    definitionMatch = false;
+    exactMatch = false;
+    startsWith = false;
+    contains = false;
+  }
+
   public String toString() {
     return getCompListDisplayString();
   }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [845] phenote/trunk/src/java/phenote

From: <mg...@us...> - 2007-08-29 18:33:44

Revision: 845
          http://obo.svn.sourceforge.net/obo/?rev=845&view=rev
Author:   mgibson
Date:     2007-08-29 11:19:08 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
added factory for characterI toward obo annot charI factory

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
    phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java
    phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
    phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java
    phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java
    phenote/trunk/src/java/phenote/datamodel/Character.java
    phenote/trunk/src/java/phenote/edit/EditManager.java
    phenote/trunk/src/java/phenote/servlet/DataInputServlet.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java

Modified: phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/dataadapter/delimited/DelimitedChar.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -9,6 +9,7 @@
 
 import phenote.datamodel.Character;
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.OntologyManager;
@@ -152,31 +153,31 @@
   /** Parse syntax line into character */
   //try just splitting at tab.
   void parseLine(String line) throws SyntaxParseException {
-		character = new Character();
+    character = CharacterIFactory.makeChar();
 //		System.out.println("input line="+line);
-		Pattern p = Pattern.compile("\t");
-		//parse based on tab...will be delimiter in future
-		String[] items = p.split(line);
-		boolean found = (items.length>0); //m.find();
+    Pattern p = Pattern.compile("\t");
+    //parse based on tab...will be delimiter in future
+    String[] items = p.split(line);
+    boolean found = (items.length>0); //m.find();
 //		System.out.println("numcols="+items.length);
-		if (!found)
-		  throw new SyntaxParseException(line); // skips whitespace lines
-		int colCount = 0;
-		int fieldCount = 0;
-		while (found) {
-		  String value = items[colCount];
-		  addDelValToChar(fieldCount,value);
-		  CharField c = Config.inst().getEnbldCharField(fieldCount);
+    if (!found)
+      throw new SyntaxParseException(line); // skips whitespace lines
+    int colCount = 0;
+    int fieldCount = 0;
+    while (found) {
+      String value = items[colCount];
+      addDelValToChar(fieldCount,value);
+      CharField c = Config.inst().getEnbldCharField(fieldCount);
 //		  System.out.println("col="+colCount+";  fieldCount="+fieldCount+"; val="+value+"; charfieldname ="+c.getName());
-	      if (isOntology(c)) {
-	        colCount++; //skip over the Name, only keep ID
-	      }
-		  colCount++;
-		  fieldCount++;
-		  found = (colCount<items.length); // if parsing last tag found will be false - at end
-		}
-	  }
-
+      if (isOntology(c)) {
+        colCount++; //skip over the Name, only keep ID
+      }
+      colCount++;
+      fieldCount++;
+      found = (colCount<items.length); // if parsing last tag found will be false - at end
+    }
+  }
+  
   class SyntaxParseException extends Exception {
     private String syntaxLine;
     SyntaxParseException(String syntaxLine) {

Modified: phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/dataadapter/fly/FlyCharacter.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -3,6 +3,7 @@
 import org.geneontology.oboedit.datamodel.OBOClass;
 
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.Character;
 import phenote.datamodel.OntologyManager;
 import phenote.datamodel.TermNotFoundException;
@@ -20,7 +21,7 @@
   }
 
   public FlyCharacter(String genotype, String proformaeEVString) {
-    character = new Character();
+    character = CharacterIFactory.makeChar();
     character.setGenotype(genotype);
     parseEVString(proformaeEVString);
   }

Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxChar.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -9,6 +9,7 @@
 
 import phenote.datamodel.Character;
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldValue;
 import phenote.datamodel.OntologyManager;
@@ -101,7 +102,7 @@
 
   /** Parse syntax line into character */
   void parseLine(String line) throws SyntaxParseException {
-    character = new Character();
+    character = CharacterIFactory.makeChar();
     Pattern p = Pattern.compile("\\S+=");//\\S+=");
     Matcher m = p.matcher(line);
     boolean found = m.find();

Modified: phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/dataadapter/phenoxml/PhenoXmlAdapter.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -28,6 +28,7 @@
 //import org.bioontologies.obd.schema.pheno.*.*;
 
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.Character;
 import phenote.datamodel.CharacterListI;
 import phenote.datamodel.CharacterList;
@@ -103,7 +104,7 @@
   
   private CharacterI newCharacterFromPhenotypeManifestation(PhenotypeManifestation pm) {
     OntologyManager ontologyManager = OntologyManager.inst();
-    CharacterI character = new Character();
+    CharacterI character = CharacterIFactory.makeChar();
     ManifestIn mi = pm.getManifestIn();
     if (mi != null) {
       String genotype = mi.getGenotype();

Modified: phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/dataadapter/worm/WormAdapter.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -16,6 +16,7 @@
 import phenote.dataadapter.CharacterListManager;
 
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.CharacterList;
 import phenote.datamodel.Character;
 import phenote.datamodel.CharFieldException;
@@ -469,7 +470,7 @@
   private CharacterListI queryPostgresCharacterReferenceList(String group, CharacterListI charList, Statement s, String joinkey, int boxI, int colI) {
       // populate a phenote character based on postgres value by joinkey, then append to character list
     try {
-      Character c1 = new Character();						// create a new character for a phenote row
+      CharacterI c1 = CharacterIFactory.makeChar();						// create a new character for a phenote row
 
       String pubID = null; String title = null; String personID = null; String name = null; String nbp = null;
 
@@ -518,7 +519,7 @@
   private CharacterListI queryPostgresCharacterMainList(String group, CharacterListI charList, Statement s, String joinkey, int boxI, int colI) {
       // populate a phenote character based on postgres value by joinkey, then append to character list
     try {
-      Character c1 = new Character();						// create a new character for a phenote row
+      CharacterI c1 = CharacterIFactory.makeChar();						// create a new character for a phenote row
 
       c1.setValue("Object Name",joinkey);					// assign the allele and the column
       String alleleColumn = joinkey+" - "+boxI+" - "+colI;

Modified: phenote/trunk/src/java/phenote/datamodel/Character.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Character.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/datamodel/Character.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -14,6 +14,9 @@
 
   private HashMap<CharField,CharFieldValue> charFieldToValue =
     new HashMap<CharField,CharFieldValue>();
+  
+  /** chould only be constrcuted from factory */
+  Character() {}
 
   // obo edit annotation that gets modified in setValues
   // private OBOEditAnntotation - get & set methods

Added: phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -0,0 +1,48 @@
+package phenote.datamodel;
+
+/** Makes instances of CharacterI, according to mode set - OBOAnnotation or Character */
+
+public class CharacterIFactory {
+  
+  private static CharacterIFactory singleton = new CharacterIFactory();
+
+  public static enum ModeEnum { CHARACTER, OBO_ANNOTATION };
+  private ModeEnum mode = ModeEnum.CHARACTER;
+
+  public static CharacterIFactory inst() { return singleton; }
+
+  /** static sugar */
+  public static CharacterI makeChar() { 
+    return inst().makeCharacter();
+  }
+
+  public CharacterI makeCharacter() {
+    // need to get mapping driver from configuration?
+    //if (mode == ModeEnum.OBO_ANNOTATION)
+    //  return new AnnotationCharacter(new BasicAnnotationMappingDriver());
+
+    // default... for now
+    return new Character();
+
+  }
+
+  public void setMode(ModeEnum me) {
+    mode = me;
+  }
+
+  public void setMode(String mode) throws FactoryEx {
+    setMode(modeForString(mode));
+  }
+
+  private ModeEnum modeForString(String mode) throws FactoryEx {
+    for (ModeEnum m : ModeEnum.values()) 
+      if (mode.equalsIgnoreCase(m.toString())) return m;
+    throw new FactoryEx("Unknown CharacterI Factory mode "+mode);
+  }
+
+  // ?? make own file
+  public static class FactoryEx extends Exception {
+    public FactoryEx(String m) { super(m); }
+  }
+}
+

Modified: phenote/trunk/src/java/phenote/edit/EditManager.java
===================================================================
--- phenote/trunk/src/java/phenote/edit/EditManager.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/edit/EditManager.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -10,6 +10,7 @@
 import phenote.dataadapter.CharacterListManager;
 import phenote.datamodel.Character;
 import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.OntologyManager;
 
 /** The way editing works is gui makes update transaction (see CharFieldGui and
@@ -119,7 +120,7 @@
   public void addInitialCharacter() {
     //AddTransaction at = new AddTransaction(new Character());
     //at.editModel();
-    addCharacter(new Character(), false);
+    addCharacter(CharacterIFactory.makeChar(), false);
     // no addTransaction(at)!
     //return at;
   }
@@ -127,7 +128,7 @@
   /** same as addInitialChar except we record the adding in the transaction list
       as it can be undone */
   public void addNewCharacter() {
-    addCharacter(new Character(), true);
+    addCharacter(CharacterIFactory.makeChar(), true);
     //addTransaction(at);
   }
 

Modified: phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/DataInputServlet.java	2007-08-29 18:07:26 UTC (rev 844)
+++ phenote/trunk/src/java/phenote/servlet/DataInputServlet.java	2007-08-29 18:19:08 UTC (rev 845)
@@ -12,7 +12,8 @@
 
 import org.apache.log4j.Logger;
 
-import phenote.datamodel.Character;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterIFactory;
 import phenote.datamodel.CharFieldException;
 import phenote.datamodel.TermNotFoundException;
 import phenote.edit.EditManager;
@@ -29,7 +30,7 @@
     System.out.println("got get" +request);
     LOG.debug("servlet doGet " + new Date());
     
-    Character ch = new Character();
+    CharacterI ch = CharacterIFactory.makeChar();
     Enumeration e = request.getParameterNames();
     while (e.hasMoreElements()) {
       Object o = e.nextElement();


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [847] phenote/trunk/conf/antibody.cfg

From: <nl...@us...> - 2007-08-29 18:21:23

Revision: 847
          http://obo.svn.sourceforge.net/obo/?rev=847&view=rev
Author:   nlw
Date:     2007-08-29 11:21:26 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
added stage to this configuration

Modified Paths:
--------------
    phenote/trunk/conf/antibody.cfg

Modified: phenote/trunk/conf/antibody.cfg
===================================================================
--- phenote/trunk/conf/antibody.cfg	2007-08-29 18:21:13 UTC (rev 846)
+++ phenote/trunk/conf/antibody.cfg	2007-08-29 18:21:26 UTC (rev 847)
@@ -44,6 +44,9 @@
   <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150">
     <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" name="Quality"/>
   </ns:field>
+  <ns:field name="Stage" syntax-abbrev="stage">
+    <ns:ontology name="stage" file="fly_development.obo"/>
+  </ns:field>
   <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
   <!-- ******************** REVISION HISTORY *********************** --> 
   <!-- 08.29.2007 - initial configuration for White group -->


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [846] phenote/trunk/src/java/phenote

From: <ba...@us...> - 2007-08-29 18:21:10

Revision: 846
          http://obo.svn.sourceforge.net/obo/?rev=846&view=rev
Author:   balhoff
Date:     2007-08-29 11:21:13 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
Striping for table rows on Mac.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-29 18:19:08 UTC (rev 845)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-29 18:21:13 UTC (rev 846)
@@ -201,6 +201,7 @@
       this.characterTemplateTable.setModel(this.tableModel);
       this.characterTemplateTable.setSelectionModel(new SelectionManagerListSelectionModel(this.characterListManager, this.editManager, this.selectionManager));
       this.characterTemplateTable.getTableHeader().addMouseListener(new TableSortingAdapter(this.characterTemplateTable, this.tableModel));
+      this.characterTemplateTable.putClientProperty("Quaqua.Table.style", "striped");
       FieldPanel fieldPanel = new FieldPanel(true, false, this.representedGroup, this.selectionManager, this.editManager);
       this.charFieldPanelContainer.add(fieldPanel);
       TermInfo termInfo = new TermInfo(this.selectionManager);

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-29 18:19:08 UTC (rev 845)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-29 18:21:13 UTC (rev 846)
@@ -114,6 +114,7 @@
     charJTable.getSelectionModel().addListSelectionListener(isl);
     charJTable.setRowSelectionInterval(0,0); // select 1st row
     charJTable.getTableHeader().addMouseListener(new TableSortingAdapter(this.charJTable, this.characterTableModel));
+    charJTable.putClientProperty("Quaqua.Table.style", "striped");
 
     JScrollPane tableScroll = new JScrollPane(charJTable);
     verticalScrollBar = tableScroll.getVerticalScrollBar();//needed for scroll to new


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [844] phenote/trunk/conf/antibody.cfg

From: <nl...@us...> - 2007-08-29 18:07:58

Revision: 844
          http://obo.svn.sourceforge.net/obo/?rev=844&view=rev
Author:   nlw
Date:     2007-08-29 11:07:26 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
small changes to antibody config; including always update from repository

Modified Paths:
--------------
    phenote/trunk/conf/antibody.cfg

Modified: phenote/trunk/conf/antibody.cfg
===================================================================
--- phenote/trunk/conf/antibody.cfg	2007-08-29 16:39:40 UTC (rev 843)
+++ phenote/trunk/conf/antibody.cfg	2007-08-29 18:07:26 UTC (rev 844)
@@ -1,43 +1,51 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--*********************** CONFIG INFO **************************-->
-<ns:phenote-configuration version="setVersionWith-Dphenote.version=x.y-betaz" name="Antibody Configuration" author="Nicole Washington" description="This config is for the use of the White group as part of the modENCODE project.  The objective it to record the phenotypes resulting from antibody stains on embryos, and possibly on western blots, as part of their antibody production pipeline." xmlns:ns="phenote/config/xml">
-  <!--*********************** SETTINGS ****************************-->
-  <!--ns:master-to-local-config mode="WIPEOUT" when="NEVER" 
-     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/antibody.cfg" /-->
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration xmlns:ns="phenote/config/xml" version="1.3.1"
+			  name="Antibody Configuration"
+			  author="Nicole Washington"
+			  description="This config is for the use of the White group as part of the modENCODE project.  The objective it to record the phenotypes resulting from antibody stains on embryos, and possibly on western blots, as part of their antibody production pipeline.">
+
+  <!-- *********************** SETTINGS **************************** -->
+  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/antibody.cfg" />
   <ns:log config-file="conf/log4j-standalone.xml"/>
+
   <ns:uvic-graph enable="false"/>
   <ns:term-history enable="false"/>
-  <ns:auto-update-ontologies enable="true"/>
-  <!--true=update; false=don't update-->
+  <ns:auto-update-ontologies enable="true"/>  
+    <!--true=update; false=don't update-->
   <ns:update-timer timer="0"/>
-  <!--set to 0 if you want to bypass the check; time in seconds-->
+    <!--set to 0 if you want to bypass the check; time in seconds-->
   <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
-  <!--********************* FILE ADAPTERS **************************-->
-  <!--be sure to include at least one enabled file adapter-->
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+
+  <!-- ********************* FILE ADAPTERS ************************** -->
+  <!-- be sure to include at least one enabled file adapter -->
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>  
   <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="false"/>
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
-  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
-  <!--******************** FIELD DEFINITIONS ***********************-->
+
+
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
   <!--The order of the fields is important, and will display in the order 
   listed here.  If a repository location is given as the filename (ie 
   "http://www.your-repository.com/your_obo_file.obo"), then this site 
-  will be checked for updates-->
-  <ns:field name="AntibodyID" syntax-abbrev="Ab" enable="true" type="FREE_TEXT" colwidth="150"/>
-  <ns:field name="PictureID" syntax-abbrev="Pic" enable="true" type="FREE_TEXT" colwidth="150"/>
-  <ns:field name="Expression Location" syntax-abbrev="Loc" enable="true" type="TERM" colwidth="434">
+  will be checked for updates -->
+  
+  <ns:field name="AntibodyID" syntax-abbrev="Ab" enable="true"/>
+  <ns:field name="Dilution" syntax-abbrev="Dil" enable="true"/>
+  <ns:field name="PictureID" syntax-abbrev="Pic" enable="true"/>
+  <ns:field name="Expression" syntax-abbrev="E" enable="true">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
     <ns:ontology name="Fly" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy.obo"/>
     <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
     <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
     <ns:ontology name="SP" file="spatial.obo"/>
   </ns:field>
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150" type="TERM">
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150">
     <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" name="Quality"/>
   </ns:field>
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true" type="FREE_TEXT" colwidth="300"/>
-  <!--******************** REVISION HISTORY ***********************-->
-  <!--08.29.2007 - initial configuration for White group-->
-  <ns:group name="default"/>
-  <ns:data-input-servlet/>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <!-- ******************** REVISION HISTORY *********************** --> 
+  <!-- 08.29.2007 - initial configuration for White group -->
+
 </ns:phenote-configuration>
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [843] phenote/trunk/conf/antibody.cfg

From: <nl...@us...> - 2007-08-29 16:40:34

Revision: 843
          http://obo.svn.sourceforge.net/obo/?rev=843&view=rev
Author:   nlw
Date:     2007-08-29 09:39:40 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
here's a basic configuration for the white group to record their antibody staining results.  will need modificiation...

Added Paths:
-----------
    phenote/trunk/conf/antibody.cfg

Added: phenote/trunk/conf/antibody.cfg
===================================================================
--- phenote/trunk/conf/antibody.cfg	                        (rev 0)
+++ phenote/trunk/conf/antibody.cfg	2007-08-29 16:39:40 UTC (rev 843)
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--*********************** CONFIG INFO **************************-->
+<ns:phenote-configuration version="setVersionWith-Dphenote.version=x.y-betaz" name="Antibody Configuration" author="Nicole Washington" description="This config is for the use of the White group as part of the modENCODE project.  The objective it to record the phenotypes resulting from antibody stains on embryos, and possibly on western blots, as part of their antibody production pipeline." xmlns:ns="phenote/config/xml">
+  <!--*********************** SETTINGS ****************************-->
+  <!--ns:master-to-local-config mode="WIPEOUT" when="NEVER" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/antibody.cfg" /-->
+  <ns:log config-file="conf/log4j-standalone.xml"/>
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+  <ns:auto-update-ontologies enable="true"/>
+  <!--true=update; false=don't update-->
+  <ns:update-timer timer="0"/>
+  <!--set to 0 if you want to bypass the check; time in seconds-->
+  <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+  <!--********************* FILE ADAPTERS **************************-->
+  <!--be sure to include at least one enabled file adapter-->
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="false"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/>
+  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
+  <!--******************** FIELD DEFINITIONS ***********************-->
+  <!--The order of the fields is important, and will display in the order 
+  listed here.  If a repository location is given as the filename (ie 
+  "http://www.your-repository.com/your_obo_file.obo"), then this site 
+  will be checked for updates-->
+  <ns:field name="AntibodyID" syntax-abbrev="Ab" enable="true" type="FREE_TEXT" colwidth="150"/>
+  <ns:field name="PictureID" syntax-abbrev="Pic" enable="true" type="FREE_TEXT" colwidth="150"/>
+  <ns:field name="Expression Location" syntax-abbrev="Loc" enable="true" type="TERM" colwidth="434">
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
+    <ns:ontology name="Fly" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/fly_anatomy.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
+    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
+    <ns:ontology name="SP" file="spatial.obo"/>
+  </ns:field>
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150" type="TERM">
+    <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" name="Quality"/>
+  </ns:field>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true" type="FREE_TEXT" colwidth="300"/>
+  <!--******************** REVISION HISTORY ***********************-->
+  <!--08.29.2007 - initial configuration for White group-->
+  <ns:group name="default"/>
+  <ns:data-input-servlet/>
+</ns:phenote-configuration>
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [842] phenote/tags/release-1.4-beta3/

From: <mg...@us...> - 2007-08-29 16:29:05

Revision: 842
          http://obo.svn.sourceforge.net/obo/?rev=842&view=rev
Author:   mgibson
Date:     2007-08-29 09:29:08 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
Tagging the 1.4-beta3 release of phenote - wormy stuff, comp optimizations, templater stuff, ...

Added Paths:
-----------
    phenote/tags/release-1.4-beta3/

Copied: phenote/tags/release-1.4-beta3 (from rev 841, phenote/trunk)


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [841] phenote/trunk/src/java/phenote/datamodel

From: <mg...@us...> - 2007-08-29 16:22:09

Revision: 841
          http://obo.svn.sourceforge.net/obo/?rev=841&view=rev
Author:   mgibson
Date:     2007-08-29 09:22:11 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
added johns new obo annotation CharacterI wrapper stuff
factory is coming...

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/datamodel/CharField.java
    phenote/trunk/src/java/phenote/datamodel/CharFieldEnum.java
    phenote/trunk/src/java/phenote/datamodel/Ontology.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java
    phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java
    phenote/trunk/src/java/phenote/datamodel/AnnotationMappingDriver.java
    phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java

Added: phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/AbstractCharacter.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -0,0 +1,216 @@
+package phenote.datamodel;
+
+import java.util.List;
+
+import org.geneontology.oboedit.datamodel.OBOClass;
+
+public abstract class AbstractCharacter implements CharacterI {
+
+	// this is just used for testing at this point
+	public boolean equals(CharacterI ch) {
+		for (CharField cf : getAllCharFields()) {
+			if (!eq(getValue(cf), ch.getValue(cf)))
+				return false;
+		}
+		return true;
+	}
+
+	/** check if both are null in addition to .equals() */
+	protected boolean eq(CharFieldValue c1, CharFieldValue c2) {
+		if (c1 == null && c2 == null)
+			return true;
+		if (c2 == null)
+			return false;
+		return c1.equals(c2);
+	}
+
+	public List<CharField> getAllCharFields() {
+		return OntologyManager.inst().getCharFieldList();
+	}
+
+	public CharField getCharFieldForName(String fieldName)
+			throws CharFieldException {
+		return OntologyManager.inst().getCharFieldForName(fieldName);
+	}
+
+	public OBOClass getEntity() {
+		try {
+			return getValue(getEntityField()).getTerm();
+		} catch (CharFieldException e) {
+			return null;
+		} // ??
+	}
+
+	protected CharField getEntityField() throws CharFieldException {
+		return getCharFieldForName(CharFieldEnum.ENTITY.getName());
+	}
+
+	protected CharField getGenConField() throws CharFieldException {
+		return getCharFieldForName(CharFieldEnum.GENETIC_CONTEXT.getName());
+	}
+
+	protected CharField getPubField() throws CharFieldException {
+		return getCharFieldForName(CharFieldEnum.PUB.getName());
+	}
+
+	protected CharField getQualField() throws CharFieldException {
+		return getCharFieldForName(CharFieldEnum.QUALITY.getName());
+	}
+
+	public OBOClass getGeneticContext() {
+		try {
+			return getTerm(getGenConField());
+		} catch (CharFieldException e) {
+			return null;
+		} // ??
+	}
+
+	protected OBOClass getTerm(CharField cf) {
+		if (!hasValue(cf))
+			return null; // ?? exception?
+		return getValue(cf).getOboClass();
+	}
+
+	public String getGenotype() {
+		try {
+			return getValueString(getGenotypeField());
+		} catch (CharFieldException e) {
+			return null;
+		} // ??
+	}
+
+	protected CharField getGenotypeField() throws CharFieldException {
+		return getCharFieldForName(CharFieldEnum.GENOTYPE.getName());
+	}
+
+	public String getPub() {
+		try {
+			return getValueString(getPubField());
+		} catch (CharFieldException e) {
+			return null;
+		} // ?? ""?
+	}
+
+	public OBOClass getQuality() {
+		// return quality;
+		try {
+			return getValue(getQualField()).getTerm();
+		} catch (CharFieldException e) {
+			return null;
+		} // ??
+	}
+
+	public OBOClass getTerm(String field) throws CharFieldException {
+		CharField cf = getCharFieldForName(field);
+		return getTerm(cf);
+	}
+
+	public String getValueString(CharField cf) {
+		CharFieldValue cfv = getValue(cf);
+		if (cfv.getName() == null)
+			return ""; // ?? ex?
+		return cfv.getName();
+	}
+
+	public String getValueString(String field) throws CharFieldException {
+		CharField cf = getCharFieldForName(field); // throws ex
+		if (!hasValue(cf))
+			return null; // ?? exception? ""?
+		return getValue(cf).getName();
+	}
+
+	public boolean hasGeneticContext() {
+		return getGeneticContext() != null && !getGeneticContext().equals("");
+	}
+
+	public boolean hasNoContent() {
+		for (CharField cf : getAllCharFields()) {
+			if (hasValue(cf))
+				return false;
+		}
+		return true;
+	}
+
+	/**
+	 * According to the CharacterI documentation, the methods below are garbage
+	 */
+
+	public boolean hasPub() {
+		return getPub() != null && !getPub().equals("");
+	}
+
+	public boolean hasValue(CharField cf) {
+		if (getValue(cf) == null)
+			return false;
+		return !getValue(cf).isEmpty();
+	}
+
+	public boolean hasValue(String fieldName) {
+		try {
+			return hasValue(getCharFieldForName(fieldName));
+		} catch (CharFieldException e) { // throws exception if doesnt have
+			return false;
+		}
+	}
+
+	public void setEntity(OBOClass e) {
+		try {
+			setValue(new CharFieldValue(e, this, getEntityField()));
+		} catch (CharFieldException x) {
+			throw new RuntimeException(x);
+		}
+	}
+
+	protected void setValue(CharFieldValue cfv) {
+		setValue(cfv.getCharField(), cfv);
+	}
+
+	public void setGeneticContext(OBOClass gc) {
+		try {
+			setValue(getGenConField(), gc);
+		} catch (CharFieldException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	protected void setValue(CharField cf, OBOClass term) {
+		setValue(new CharFieldValue(term, this, cf));
+	}
+
+	public void setGenotype(String gt) {
+		try {
+			setValue(getGenotypeField(), gt);
+		} catch (CharFieldException x) {
+			throw new RuntimeException(x);
+		} catch (TermNotFoundException e) {
+		} // doesnt happen for free text field
+	}
+
+	public void setPub(String p) {
+		try {
+			setValue(new CharFieldValue(p, this, getPubField()));
+		} catch (CharFieldException x) {
+			throw new RuntimeException(x);
+		}
+	}
+
+	public void setQuality(OBOClass q) {
+		try {
+			setValue(new CharFieldValue(q, this, getQualField()));
+		} catch (CharFieldException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	public void setValue(String fieldString, String valueString)
+			throws CharFieldException, TermNotFoundException {
+		CharField cf = getCharFieldForName(fieldString);
+		setValue(cf, valueString);
+	}
+
+	public void setValue(CharField cf, String s) throws TermNotFoundException {
+		CharFieldValue cfv = cf.makeValue(this, s);
+		setValue(cf, cfv);
+	}
+
+}

Added: phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/AnnotationCharacter.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -0,0 +1,143 @@
+package phenote.datamodel;
+
+import org.geneontology.oboedit.annotation.datamodel.Annotation;
+import org.geneontology.oboedit.annotation.datamodel.impl.AnnotationImpl;
+import org.geneontology.oboedit.datamodel.LinkedObject;
+import org.geneontology.oboedit.datamodel.OBOClass;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.TermUtil;
+
+public class AnnotationCharacter extends AbstractCharacter {
+
+	protected static int idgen = 0;
+
+	protected Annotation annotation;
+	protected AnnotationMappingDriver driver;
+
+	/*
+	 * Extend this method to provide more field mappings. This should be all you
+	 * need to do for simple mappings
+	 */
+	protected OBOProperty getPropertyForField(CharField cf) {
+		return driver.getPropertyForField(cf);
+	}
+
+	protected CharFieldValue getCharFieldValue(OBOClass oboClass,
+			CharacterI character, CharField field) {
+		return driver.getCharFieldValue(oboClass, character, field);
+	}
+
+	protected CharFieldValue getCharFieldValue(String s, CharacterI character,
+			CharField field) {
+		return driver.getCharFieldValue(s, character, field);
+	}
+
+	protected void setPropertyValue(Annotation annotation,
+			OBOProperty property, OBOClass value) {
+		driver.setPropertyValue(annotation, property, value);
+	}
+
+	protected void setPropertyValue(Annotation annotation,
+			OBOProperty property, String value) {
+		driver.setPropertyValue(annotation, property, value);
+	}
+
+	protected OBOProperty getDefaultRelationship() {
+		return driver.getDefaultRelationship();
+	}
+
+	protected boolean isSubjectField(CharField cf) {
+		return driver.isSubjectField(cf);
+	}
+
+	protected boolean isObjectField(CharField cf) {
+		return driver.isObjectField(cf);
+	}
+
+	protected void resetRelationshipField() {
+		if (!annotation.getRelationship().equals(getDefaultRelationship())) {
+			if (driver.getAuditHistoryMode()) {
+				driver.addHistoryItem(annotation
+						.getRelationshipChangeItem(getDefaultRelationship()));
+			}
+			if (driver.getChangeObjectsMode())
+				annotation.setRelationship(getDefaultRelationship());
+		}
+	}
+
+	public void setValue(CharField cf, CharFieldValue cfv) {
+		if (isSubjectField(cf) && cfv.isTerm()) {
+			if (driver.getAuditHistoryMode()) {
+				driver.addHistoryItem(annotation.getSubjectChangeItem(cfv
+						.getOboClass()));
+			}
+			if (driver.getChangeObjectsMode())
+				annotation.setSubject(cfv.getOboClass());
+			resetRelationshipField();
+		} else if (isObjectField(cf) && cfv.isTerm()) {
+			if (driver.getAuditHistoryMode()) {
+				driver.addHistoryItem(annotation.getObjectChangeItem(cfv
+						.getOboClass()));
+			}
+			if (driver.getChangeObjectsMode())
+				annotation.setObject(cfv.getOboClass());
+			resetRelationshipField();
+		} else {
+			OBOProperty prop = getPropertyForField(cf);
+			if (prop != null) {
+				if (cfv.isTerm()) {
+					setPropertyValue(annotation, prop, cfv.getOboClass());
+				} else {
+					setPropertyValue(annotation, prop, cfv.getName());
+				}
+			}
+		}
+	}
+
+	public AnnotationCharacter(AnnotationMappingDriver driver) {
+		this("__temp__:" + idgen++, driver);
+		annotation.setIsAnonymous(true);
+	}
+
+	public AnnotationCharacter(String id, AnnotationMappingDriver driver) {
+		this(new AnnotationImpl(id), driver);
+	}
+
+	public AnnotationCharacter(Annotation annotation, AnnotationMappingDriver driver) {
+		this.annotation = annotation;
+		this.driver = driver;
+	}
+
+	public CharFieldValue getValue(CharField cf) {
+		CharFieldValue cfv = null;
+		if (isSubjectField(cf)) {
+			LinkedObject subject = annotation.getSubject();
+			if (subject instanceof OBOClass) {
+				cfv = new CharFieldValue((OBOClass) subject, this, cf);
+			}
+		} else if (isObjectField(cf)) {
+			LinkedObject object = annotation.getObject();
+			if (object instanceof OBOClass) {
+				cfv = new CharFieldValue((OBOClass) object, this, cf);
+			}
+		} else {
+			OBOProperty prop = getPropertyForField(cf);
+			if (prop != null) {
+				Object o = TermUtil.getPropValue(annotation, prop);
+				if (o instanceof OBOClass) {
+					cfv = getCharFieldValue((OBOClass) o, this, cf);
+				} else if (o instanceof String) {
+					cfv = getCharFieldValue((String) o, this, cf);
+				}
+			}
+		}
+		if (cfv == null)
+			cfv = CharFieldValue.emptyValue(this, cf);
+		return cfv;
+	}
+
+	public CharacterI cloneCharacter() {
+		Annotation clone = (Annotation) annotation.clone();
+		return new AnnotationCharacter(clone, driver);
+	}
+}

Added: phenote/trunk/src/java/phenote/datamodel/AnnotationMappingDriver.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/AnnotationMappingDriver.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/AnnotationMappingDriver.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -0,0 +1,40 @@
+package phenote.datamodel;
+
+import java.util.List;
+
+import org.geneontology.oboedit.annotation.datamodel.Annotation;
+import org.geneontology.oboedit.datamodel.HistoryItem;
+import org.geneontology.oboedit.datamodel.OBOClass;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+
+public interface AnnotationMappingDriver {
+	public OBOProperty getPropertyForField(CharField cf);
+
+	public CharFieldValue getCharFieldValue(OBOClass oboclass,
+			CharacterI character, CharField field);
+
+	public CharFieldValue getCharFieldValue(String s, CharacterI character,
+			CharField field);
+	
+	public void setPropertyValue(Annotation annotation, OBOProperty property,
+			OBOClass value);
+	
+	public void setPropertyValue(Annotation annotation, OBOProperty property,
+			String value);
+
+	public void clearProperty(Annotation annotation, OBOProperty property);
+	
+	public OBOProperty getDefaultRelationship();
+	
+	public boolean isSubjectField(CharField cf);
+
+	public boolean isObjectField(CharField cf);
+	
+	public boolean getAuditHistoryMode();
+	
+	public boolean getChangeObjectsMode();
+	
+	public List<HistoryItem> popHistoryList();
+	
+	public void addHistoryItem(HistoryItem item);
+}

Added: phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/datamodel/BasicAnnotationMappingDriver.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -0,0 +1,142 @@
+package phenote.datamodel;
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.geneontology.oboedit.annotation.datamodel.Annotation;
+import org.geneontology.oboedit.annotation.datamodel.AnnotationOntology;
+import org.geneontology.oboedit.datamodel.Datatype;
+import org.geneontology.oboedit.datamodel.HistoryItem;
+import org.geneontology.oboedit.datamodel.IdentifiedObject;
+import org.geneontology.oboedit.datamodel.OBOClass;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.Value;
+import org.geneontology.oboedit.datamodel.history.AddPropertyValueHistoryItem;
+import org.geneontology.oboedit.datamodel.history.DeletePropertyValueHistoryItem;
+import org.geneontology.oboedit.datamodel.impl.DatatypeValueImpl;
+import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
+
+public class BasicAnnotationMappingDriver implements AnnotationMappingDriver {
+
+	protected boolean auditHistoryMode = false;
+	protected boolean changeObjectsMode = true;
+	protected List<HistoryItem> historyItems;
+
+	/**
+	 * We probably want to create a special static ontology that extends
+	 * AnnotationOntology to contain these properties. This is here just to keep
+	 * the example simple
+	 */
+	protected static final OBOProperty GENOTYPE_REL = new OBOPropertyImpl(
+			"oban:has_genotype", "has_genotype");
+	protected static final OBOProperty HAS_QUALITY_REL = new OBOPropertyImpl(
+			"pato:has_quality", "has_quality");
+
+	public OBOProperty getPropertyForField(CharField cf) {
+		if (cf.equals(CharFieldEnum.PUB.getName())) {
+			return AnnotationOntology.EVIDENCE_REL();
+		} else if (cf.equals(CharFieldEnum.GENOTYPE.getName())) {
+			return GENOTYPE_REL;
+		}
+		return null;
+	}
+
+	public List<HistoryItem> popHistoryList() {
+		List<HistoryItem> out = historyItems;
+		historyItems = new LinkedList<HistoryItem>();
+		return out;
+	}
+	
+	public CharFieldValue getCharFieldValue(OBOClass oboclass,
+			CharacterI character, CharField field) {
+		return new CharFieldValue(oboclass, character, field);
+	}
+
+	public CharFieldValue getCharFieldValue(String s, CharacterI character,
+			CharField field) {
+		return new CharFieldValue(s, character, field);
+	}
+
+	public void setPropertyValue(Annotation annotation, OBOProperty property,
+			OBOClass value) {
+		clearProperty(annotation, property);
+		if (changeObjectsMode)
+			annotation.addPropertyValue(property, value);
+		if (auditHistoryMode) {
+			historyItems.add(new AddPropertyValueHistoryItem(
+					annotation.getID(), property.getID(), value.getType()
+							.getID(), value.getID()));
+		}
+	}
+
+	public void setPropertyValue(Annotation annotation, OBOProperty property,
+			String value) {
+		clearProperty(annotation, property);
+		if (changeObjectsMode)
+			annotation.addPropertyValue(property, new DatatypeValueImpl(
+					Datatype.STRING, value));
+		if (auditHistoryMode) {
+			historyItems.add(new AddPropertyValueHistoryItem(
+					annotation.getID(), property.getID(), Datatype.STRING
+							.getID(), value));
+		}
+	}
+
+	public void clearProperty(Annotation annotation, OBOProperty property) {
+		Collection<Value> values = new LinkedList<Value>(annotation
+				.getValues(property));
+		for (Value v : values) {
+			if (auditHistoryMode) {
+				String stringVal = null;
+				if (v.getType() instanceof Datatype) {
+					stringVal = ((Datatype) v.getType()).getString(v);
+				} else if (v instanceof IdentifiedObject) {
+					stringVal = ((IdentifiedObject) v).getID();
+				}
+				if (stringVal != null)
+					historyItems.add(new DeletePropertyValueHistoryItem(
+							annotation.getID(), property.getID(), v.getType()
+									.getID(), stringVal));
+			}
+			if (changeObjectsMode)
+				annotation.removePropertyValue(property, v);
+		}
+	}
+
+	public OBOProperty getDefaultRelationship() {
+		return HAS_QUALITY_REL;
+	}
+
+	public boolean isSubjectField(CharField cf) {
+		return CharFieldEnum.ENTITY.getName().equals(cf);
+	}
+
+	public boolean isObjectField(CharField cf) {
+		return CharFieldEnum.QUALITY.getName().equals(cf);
+	}
+
+	public boolean getAuditHistoryMode() {
+		return auditHistoryMode;
+	}
+
+	public void setAuditHistoryMode(boolean auditHistoryMode) {
+		this.auditHistoryMode = auditHistoryMode;
+		if (auditHistoryMode && historyItems == null)
+			historyItems = new LinkedList<HistoryItem>();
+		else if (!auditHistoryMode)
+			historyItems = null;
+	}
+
+	public boolean getChangeObjectsMode() {
+		return changeObjectsMode;
+	}
+
+	public void setChangeObjectsMode(boolean changeObjectsMode) {
+		this.changeObjectsMode = changeObjectsMode;
+	}
+
+	public void addHistoryItem(HistoryItem item) {
+		historyItems.add(item);		
+	}
+}

Modified: phenote/trunk/src/java/phenote/datamodel/CharField.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharField.java	2007-08-29 15:55:50 UTC (rev 840)
+++ phenote/trunk/src/java/phenote/datamodel/CharField.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -184,7 +184,7 @@
     throws TermNotFoundException {
 
     // FREE TEXT FIELD
-    if (!hasOntologies())
+    if (!hasOntologies()) // -> !isTerm() or isFreeText()
       return new CharFieldValue(valueString,c,this);
 
     // ONTOLOGY

Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldEnum.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldEnum.java	2007-08-29 15:55:50 UTC (rev 840)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldEnum.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -16,54 +16,11 @@
     or check this - i dont think there is */
 public enum CharFieldEnum {
 
-  PUB("Pub") {
-    public void setValue(CharacterI c, CharFieldValue v) {
-      c.setPub(v.getName());
-    }
-    public CharFieldValue getValue(CharacterI c) {
-      return new CharFieldValue(c.getPub(),c,this);
-    }
-  },
-  GENOTYPE("Genotype") { // genotype? default?
-    public void setValue(CharacterI c, CharFieldValue v) {
-      c.setGenotype(v.getName());
-    }
-    public CharFieldValue getValue(CharacterI c) {
-      return new CharFieldValue(c.getGenotype(),c,this);
-    }
-  },
-  ALLELE("Allele"),
-  GENETIC_CONTEXT("Genetic Context") {
-    public void setValue(CharacterI c, CharFieldValue v) {
-      c.setGeneticContext(v.getOboClass());
-    }
-    public CharFieldValue getValue(CharacterI c) {
-      return new CharFieldValue(c.getGeneticContext(),c,this);
-    }
-  },
-  ENTITY("Entity") {
-    public void setValue(CharacterI c, CharFieldValue v) {
-        c.setEntity(v.getOboClass());
-    }
-    public CharFieldValue getValue(CharacterI c) {
-      return new CharFieldValue(c.getEntity(),c,this);
-    }
-  },
-  QUALITY("Quality") {
-    public void setValue(CharacterI c, CharFieldValue v) {
-        c.setQuality(v.getOboClass());
-    }
-    public CharFieldValue getValue(CharacterI c) {
-      return new CharFieldValue(c.getQuality(),c,this);
-    }
-  },
+  PUB("Pub"), GENOTYPE("Genotype"), ALLELE("Allele"), GENETIC_CONTEXT("Genetic Context"),
+  ENTITY("Entity"), QUALITY("Quality"),
   /** Its questionable if relationship belongs here ??? */
-  RELATIONSHIP("Relationship") {
-    public void setValue(CharacterI c, CharFieldValue v) {}
-    public CharFieldValue getValue(CharacterI c) { return null; }
-  };
+  RELATIONSHIP("Relationship");
   
-  
   // CHAR FIELD ENUM vars & methods (make its own class!)
   private final String name;
   private CharFieldEnum(String name) { this.name = name; }

Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-08-29 15:55:50 UTC (rev 840)
+++ phenote/trunk/src/java/phenote/datamodel/Ontology.java	2007-08-29 16:22:11 UTC (rev 841)
@@ -134,9 +134,9 @@
 
   public String getName() { return name; }
 
-  /** returns null if dont have class for id, throws OntologyException if id is not
+  /** throws TermNotFoundException if id is not
       found 
-      this was only searching non-obsolete terms changing it to also include obsoletes*/
+      searches non-obsolete & obsoletes*/
   public OBOClass getTerm(String id) throws TermNotFoundException {
     // this aint right - if its a slim should only search slim
     //OBOClass oc = oboSession.getTerm(id);
@@ -149,6 +149,9 @@
         return obs;
     }
     //if (term == null)
+
+    // if (danglerMode()) return new Dangler();
+
     throw new TermNotFoundException(id +" id not found in ontology "+name);
     //return oc;
   }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [840] phenote/trunk/src/java/phenote

From: <ba...@us...> - 2007-08-29 15:55:49

Revision: 840
          http://obo.svn.sourceforge.net/obo/?rev=840&view=rev
Author:   balhoff
Date:     2007-08-29 08:55:50 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
Added column sorting to CharacterTemplate table.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
    phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java

Added Paths:
-----------
    phenote/trunk/src/java/phenote/gui/SortableTableModel.java
    phenote/trunk/src/java/phenote/gui/TableSortingAdapter.java

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-29 13:56:22 UTC (rev 839)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -27,6 +27,7 @@
 import phenote.datamodel.CharacterI;
 import phenote.edit.EditManager;
 import phenote.gui.MenuManager;
+import phenote.gui.TableSortingAdapter;
 import phenote.gui.TermInfo;
 import phenote.gui.field.FieldPanel;
 import phenote.gui.selection.SelectionManager;
@@ -198,7 +199,8 @@
     try {
       JComponent component = (JComponent)swix.render(FileUtil.findUrl("character_template.xml"));
       this.characterTemplateTable.setModel(this.tableModel);
-      this.characterTemplateTable.setSelectionModel(new SelectionManagerListSelectionModel(this.characterListManager, this.editManager, this.selectionManager));  
+      this.characterTemplateTable.setSelectionModel(new SelectionManagerListSelectionModel(this.characterListManager, this.editManager, this.selectionManager));
+      this.characterTemplateTable.getTableHeader().addMouseListener(new TableSortingAdapter(this.characterTemplateTable, this.tableModel));
       FieldPanel fieldPanel = new FieldPanel(true, false, this.representedGroup, this.selectionManager, this.editManager);
       this.charFieldPanelContainer.add(fieldPanel);
       TermInfo termInfo = new TermInfo(this.selectionManager);

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-29 13:56:22 UTC (rev 839)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -15,14 +15,16 @@
 import phenote.dataadapter.CharListChangeEvent;
 import phenote.dataadapter.CharListChangeListener;
 import phenote.dataadapter.CharacterListManager;
+import phenote.datamodel.CharField;
 import phenote.datamodel.CharFieldException;
 import phenote.datamodel.CharacterI;
 import phenote.edit.CharChangeEvent;
 import phenote.edit.CharChangeListener;
 import phenote.edit.EditManager;
+import phenote.gui.SortableTableModel;
 
 @SuppressWarnings("serial")
-public class CharacterTemplateTableModel extends AbstractTableModel implements CharChangeListener, CharListChangeListener, TemplateChoiceListener {
+public class CharacterTemplateTableModel extends AbstractTableModel implements CharChangeListener, CharListChangeListener, TemplateChoiceListener, SortableTableModel {
   
   private String representedGroup;
   private CharacterListManager characterListManager;
@@ -149,6 +151,24 @@
     this.setMarkedCharacters(source.getChosenTemplates(Collections.unmodifiableList(this.getAllCharacters())));
   }
   
+  public void sortOnColumn(int column) {
+    final String fieldName = this.getColumnName(column);
+    // right now we cannot sort by the checkmarked column, unfortunately
+    if (fieldName.equals(CharacterTemplateTableModel.SELECTED_COLUMN_NAME)) return;
+    final CharacterI aCharacter;
+    if (this.getRowCount() < 1) {
+      return;
+    } else {
+      aCharacter = this.getCharacterAtRow(0);
+    }
+    try {
+      final CharField charField = aCharacter.getCharFieldForName(fieldName);
+      this.characterListManager.getCharacterList().sortBy(charField);
+    } catch (CharFieldException e) {
+      this.getLogger().error("Could not find CharField to sort by", e);
+    }
+  }
+  
   private CharacterI getCharacterAtRow(int row) {
     return this.characterListManager.getCharacterList().get(row);
   }

Modified: phenote/trunk/src/java/phenote/gui/CharacterTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableModel.java	2007-08-29 13:56:22 UTC (rev 839)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableModel.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -18,7 +18,7 @@
  *  table model for table of characters. currently holds list of characters - this should
  be moved to datamodel - CharacterList object? CharacterSession? Phenotype?
  */
-class CharacterTableModel extends AbstractTableModel {
+class CharacterTableModel extends AbstractTableModel implements SortableTableModel {
 
   //private int rowCount = 0;
   // todo - get this from data adapter/model - especially for loaded
@@ -185,11 +185,14 @@
   /** hmmmm... do we sort data or some view of data, view is probably cleaner
       but for now just sort data itself? dont yet have separate view objects to
       sort */
-  void setSortKey(int col) {
-    CharField cf = cfg().getEnbldCharField(col);
-    characterList.sortBy(cf); // ???
+  public void sortOnColumn(int column) {
+    CharField cf = cfg().getEnbldCharField(column);
+    characterList.sortBy(cf);
     fireTableDataChanged();
   }
+
+
+
   private Logger log;
   private Logger log() {
     if (log == null) log = Logger.getLogger(getClass());

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-29 13:56:22 UTC (rev 839)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -113,7 +113,7 @@
     CharacterSelectionListener isl = new CharacterSelectionListener();
     charJTable.getSelectionModel().addListSelectionListener(isl);
     charJTable.setRowSelectionInterval(0,0); // select 1st row
-    charJTable.getTableHeader().addMouseListener(new TableSorter());
+    charJTable.getTableHeader().addMouseListener(new TableSortingAdapter(this.charJTable, this.characterTableModel));
 
     JScrollPane tableScroll = new JScrollPane(charJTable);
     verticalScrollBar = tableScroll.getVerticalScrollBar();//needed for scroll to new
@@ -499,24 +499,6 @@
   	}	
   }
   
-
-  private class TableSorter extends MouseAdapter {
-    public void mouseClicked(MouseEvent e) {
-      if (e.getClickCount() != 1) return; // ?
-      Point p = e.getPoint();
-      int viewColumnIndex = charJTable.getTableHeader().columnAtPoint(p);
-      int modelColumnIndex = charJTable.convertColumnIndexToModel(viewColumnIndex);
-      if (modelColumnIndex == -1) return;
-      // shift for descending
-      //  int shiftPressedInt = e.getModifiers()&InputEvent.SHIFT_MASK;
-      //  boolean shiftPressed = (shiftPressedInt != 0);
-      // boolean descending = shiftPressed;
-      //if (model.defaultSortingIsDescending(column))descending = !descending;dont have
-      characterTableModel.setSortKey(modelColumnIndex); //, descending);
-      //table.requestFocus();
-      
-    }
-  }
   private void setPoint (Point p) {
   	currentMousePoint= p;
   	return;

Added: phenote/trunk/src/java/phenote/gui/SortableTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SortableTableModel.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/gui/SortableTableModel.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -0,0 +1,7 @@
+package phenote.gui;
+
+public interface SortableTableModel {
+
+  public void sortOnColumn(int column);
+  
+}

Added: phenote/trunk/src/java/phenote/gui/TableSortingAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TableSortingAdapter.java	                        (rev 0)
+++ phenote/trunk/src/java/phenote/gui/TableSortingAdapter.java	2007-08-29 15:55:50 UTC (rev 840)
@@ -0,0 +1,28 @@
+package phenote.gui;
+
+import java.awt.Point;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.JTable;
+
+public class TableSortingAdapter extends MouseAdapter {
+  private JTable table;
+  private SortableTableModel model;
+
+  public TableSortingAdapter(JTable theTable, SortableTableModel theModel) {
+    super();
+    this.table = theTable;
+    this.model = theModel;
+  }
+  
+  public void mouseClicked(MouseEvent e) {
+    if (e.getClickCount() != 1) return;
+    final Point p = e.getPoint();
+    final int viewColumnIndex = this.table.getTableHeader().columnAtPoint(p);
+    final int modelColumnIndex = this.table.convertColumnIndexToModel(viewColumnIndex);
+    if (modelColumnIndex == -1) return;
+    this.model.sortOnColumn(modelColumnIndex);
+  }
+  
+}


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [839] phenote/trunk/src/java/phenote/gui/ CharacterTablePanel.java

From: <ba...@us...> - 2007-08-29 13:56:19

Revision: 839
          http://obo.svn.sourceforge.net/obo/?rev=839&view=rev
Author:   balhoff
Date:     2007-08-29 06:56:22 -0700 (Wed, 29 Aug 2007)

Log Message:
-----------
Bugfix - column sorting did not work properly if the user previously dragged the columns into a different order.  When the user clicked on column header i, the column that was originally at index i was being sorted instead of the column currently at index i.

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java

Modified: phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-28 20:39:17 UTC (rev 838)
+++ phenote/trunk/src/java/phenote/gui/CharacterTablePanel.java	2007-08-29 13:56:22 UTC (rev 839)
@@ -504,14 +504,15 @@
     public void mouseClicked(MouseEvent e) {
       if (e.getClickCount() != 1) return; // ?
       Point p = e.getPoint();
-      int col = charJTable.getTableHeader().columnAtPoint(p);
-      if (col == -1) return;
+      int viewColumnIndex = charJTable.getTableHeader().columnAtPoint(p);
+      int modelColumnIndex = charJTable.convertColumnIndexToModel(viewColumnIndex);
+      if (modelColumnIndex == -1) return;
       // shift for descending
       //  int shiftPressedInt = e.getModifiers()&InputEvent.SHIFT_MASK;
       //  boolean shiftPressed = (shiftPressedInt != 0);
       // boolean descending = shiftPressed;
       //if (model.defaultSortingIsDescending(column))descending = !descending;dont have
-      characterTableModel.setSortKey(col); //, descending);
+      characterTableModel.setSortKey(modelColumnIndex); //, descending);
       //table.requestFocus();
       
     }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [838] phenote/trunk

From: <ba...@us...> - 2007-08-28 20:39:20

Revision: 838
          http://obo.svn.sourceforge.net/obo/?rev=838&view=rev
Author:   balhoff
Date:     2007-08-28 13:39:17 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
Added ability to unmark selected rows in character template.

Modified Paths:
--------------
    phenote/trunk/conf/character_template.xml
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java

Modified: phenote/trunk/conf/character_template.xml
===================================================================
--- phenote/trunk/conf/character_template.xml	2007-08-28 19:57:33 UTC (rev 837)
+++ phenote/trunk/conf/character_template.xml	2007-08-28 20:39:17 UTC (rev 838)
@@ -13,13 +13,14 @@
 	    </scrollpane>
 	    <panel id="buttonPanel">
 	    	<gridbagconstraints gridx="0" gridy="1" weightx="1" insets="10,10,10,10"/>
-	        <button id="addButton" text="New" action="addNewCharacter"/>
-	        <button id="duplicateButton" text="Duplicate" action="duplicateSelectedCharacters"/>
-	        <button id="deleteButton" text="Delete" action="deleteSelectedCharacters"/>
-	        <button id="undoButton" text="Undo" action="undo"/>
-	        <button id="markButton" text="Mark Selected" action="markSelectedCharacters"/>
-	        <button id="invertSelectionButton" text="Invert Marked" action="invertMarkedCharacters"/>
-	        <button id="generateButton" text="Generate Characters" action="generateCharacters"/>
+	        <button id="addButton" text="New" action="addNewCharacter" toolTipText="Add new row"/>
+	        <button id="duplicateButton" text="Duplicate" action="duplicateSelectedCharacters" toolTipText="Duplicate selected rows"/>
+	        <button id="deleteButton" text="Delete" action="deleteSelectedCharacters" toolTipText="Delete selected rows"/>
+	        <button id="undoButton" text="Undo" action="undo" toolTipText="Undo previous action"/>
+	        <button id="markButton" text="Mark" action="markSelectedCharacters" toolTipText="Mark selected rows for use"/>
+	        <button id="unmarkButton" text="Unmark" action="unmarkSelectedCharacters" toolTipText="Unmark selected rows for use"/>
+	        <button id="invertSelectionButton" text="Invert" action="invertMarkedCharacters" toolTipText="Invert rows marked for use"/>
+	        <button id="generateButton" text="Generate Characters" action="generateCharacters" toolTipText="Generate characters in the main window from marked templates"/>
 	    </panel>
 	</panel>
 </splitpane>
\ No newline at end of file

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-28 19:57:33 UTC (rev 837)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-28 20:39:17 UTC (rev 838)
@@ -102,9 +102,13 @@
   }
   
   public void markSelectedCharacters() {
-    this.tableModel.markCharactersInRows(this.characterTemplateTable.getSelectedRows());
+    this.tableModel.setCharactersInRowsAreMarked(this.characterTemplateTable.getSelectedRows(), true);
   }
   
+  public void unmarkSelectedCharacters() {
+    this.tableModel.setCharactersInRowsAreMarked(this.characterTemplateTable.getSelectedRows(), false);
+  }
+  
   public void undo() {
     this.editManager.undo();
   }

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-28 19:57:33 UTC (rev 837)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-28 20:39:17 UTC (rev 838)
@@ -77,9 +77,9 @@
     }
   }
   
-  public void markCharactersInRows(int[] rows) {
+  public void setCharactersInRowsAreMarked(int[] rows, boolean marked) {
     for (int row : rows) {
-      this.setCharacterIsMarked(this.getCharacterAtRow(row), true);
+      this.setCharacterIsMarked(this.getCharacterAtRow(row), marked);
     }
   }
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [837] phenote/trunk/src/java/phenote/gui/field

From: <mg...@us...> - 2007-08-28 19:57:33

Revision: 837
          http://obo.svn.sourceforge.net/obo/?rev=837&view=rev
Author:   mgibson
Date:     2007-08-28 12:57:33 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
if min comp chars is not 0 then dont preload the completion field 
this seems sensible and it makes post comp gui come up much faster
as that preloading was bogging it down
pre loading is really for fields without that many terms
should have a config for it - but non zero min-comp-chars serves as
such for the moment - and maybe is sufficient
though i think eventually if a user does hit down arrow on empty (or less
than min) it should do completion - override min

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
    phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 19:36:48 UTC (rev 836)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 19:57:33 UTC (rev 837)
@@ -48,7 +48,12 @@
   private int minCompChars = 0;
 
   protected AbstractAutoCompList(CharField cf) {
+    this(cf,0); // minCompChars = 0
+  }
+
+  protected AbstractAutoCompList(CharField cf,int minCompChars) {
     super(cf);
+    setMinCompChars(minCompChars);
     init();
   }
 
@@ -60,7 +65,10 @@
     jComboBox.addActionListener(new ComboBoxActionListener());
     compListSearcher = new CompListSearcher(getCharField().getOntologyList());
     // init with all terms if config.showAllOnEmptyInput...
-    doCompletion(false); // dont show popup - we dont have a gui yet, just populating
+    if (getMinCompChars() == 0) {
+      boolean showPopupWithComp = false; // dont show popup -
+      doCompletion(showPopupWithComp);  //we dont have a gui yet, just populating
+    }
   }
 
   public void setMinCompChars(int minChars) { minCompChars = minChars; }

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 19:36:48 UTC (rev 836)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 19:57:33 UTC (rev 837)
@@ -63,10 +63,10 @@
   
 
   /** CharFieldGui for main window not post comp box - factory method */
-  static CharFieldGui makeCharFieldGui(CharField charField) {
+  static CharFieldGui makeCharFieldGui(CharField charField,int minCompChars) {
     if (charField.isTerm()) { //hasOntologies()) {
       //return new TermCompList(charField,sp,true); // enable listeners
-      TermCompList t = new TermCompList(charField);
+      TermCompList t = new TermCompList(charField,minCompChars);
       //t.setSearchParams(sp);
       t.allowPostCompButton(true);
       return t;
@@ -93,11 +93,12 @@
 
   /** make term completion lists for post comp window (genus & diff), they dont listen
       to selection nor edit model - isolated */
-  static CharFieldGui makePostCompTermList(CharField cf,String label) {
+  static CharFieldGui makePostCompTermList(CharField cf,String label,
+                                           int minCompChars) {
     // false - no listeners(dont edit model), false - dont add comp button
     // eventually adding comp button come from config for recursive comp
     //boolean allowPostCompBut = false;
-    TermCompList t =  new TermCompList(cf);
+    TermCompList t =  new TermCompList(cf,minCompChars);
     //t.setSearchParams(sp);
     // t.isInSeparateWindow(true) or t.isolate(true)??
     t.enableEditModel(false);

Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-08-28 19:36:48 UTC (rev 836)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-08-28 19:57:33 UTC (rev 837)
@@ -133,11 +133,8 @@
         fieldPanel = new JPanel(new GridBagLayout());
         jTabbedPane.addTab("Tab "+tab++,fieldPanel);
       }
-      CharFieldGui gui = CharFieldGui.makeCharFieldGui(charField);
-      if (charField.isTerm()) {
-        int minCompChars = Config.inst().getMinCompChars(fieldNum);
-        gui.setMinCompChars(minCompChars);
-      }
+      int minCompChars = Config.inst().getMinCompChars(fieldNum);
+      CharFieldGui gui = CharFieldGui.makeCharFieldGui(charField,minCompChars);
       ++fieldNum;
       gui.setSelectionManager(this.selectionManager);
       gui.setEditManager(this.editManager);

Modified: phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-08-28 19:36:48 UTC (rev 836)
+++ phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-08-28 19:57:33 UTC (rev 837)
@@ -81,8 +81,7 @@
     //compFieldPanel.setSearchParams(searchParams);
     
     // MAIN GENUS TERM
-    genusField = CharFieldGui.makePostCompTermList(charField,"Genus");
-    genusField.setMinCompChars(minCompChars);
+    genusField = CharFieldGui.makePostCompTermList(charField,"Genus",minCompChars);
     genusField.setSelectionManager(this.selectionManager);
     compFieldPanel.addCharFieldGuiToPanel(genusField);
 
@@ -130,7 +129,7 @@
       relField.setEditManager(PostCompGui.this.editManager);
       relField.setSelectionManager(PostCompGui.this.selectionManager);
       compFieldPanel.addCharFieldGuiToPanel(relField);
-      diffField = CharFieldGui.makePostCompTermList(charField,"Differentia");
+      diffField = CharFieldGui.makePostCompTermList(charField,"Differentia",minCompChars);
       diffField.setEditManager(PostCompGui.this.editManager);
       diffField.setSelectionManager(PostCompGui.this.selectionManager);
       compFieldPanel.addCharFieldGuiToPanel(diffField);

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-08-28 19:36:48 UTC (rev 836)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-08-28 19:57:33 UTC (rev 837)
@@ -34,8 +34,9 @@
   private JButton postCompButton;
 
 
-  protected TermCompList(CharField cf) {
-    super(cf);
+  protected TermCompList(CharField cf,int minCompChars) {
+    // AbstractAutoCompList constructor - does pre-populating if minCompChars==0
+    super(cf,minCompChars);
     init();
   }
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [836] phenote/trunk/src/java/phenote/gui/field

From: <mg...@us...> - 2007-08-28 19:36:48

Revision: 836
          http://obo.svn.sourceforge.net/obo/?rev=836&view=rev
Author:   mgibson
Date:     2007-08-28 12:36:48 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
send min completion chars to post comp as post comp wasnt adhering

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 19:22:41 UTC (rev 835)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 19:36:48 UTC (rev 836)
@@ -64,6 +64,7 @@
   }
 
   public void setMinCompChars(int minChars) { minCompChars = minChars; }
+  public int getMinCompChars() { return minCompChars; }
 
   protected Component getUserInputGui() { return jComboBox; }
 

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 19:22:41 UTC (rev 835)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 19:36:48 UTC (rev 836)
@@ -525,6 +525,7 @@
 
   /** no op - override in term completion gui */
   public void setMinCompChars(int minCompChars) {}
+  public int getMinCompChars() { return 0; }
 
   private Logger log;
   private Logger log() {

Modified: phenote/trunk/src/java/phenote/gui/field/PostCompGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-08-28 19:22:41 UTC (rev 835)
+++ phenote/trunk/src/java/phenote/gui/field/PostCompGui.java	2007-08-28 19:36:48 UTC (rev 836)
@@ -57,54 +57,22 @@
   private EditManager editManager;
   private SelectionManager selectionManager;
   private Frame owner;
+  /** # of chars to type to get completion in genus & diff - do we need for relation? */
+  private int minCompChars=0;
   
   
-  PostCompGui(CharField charField, EditManager eManager, SelectionManager selManager, Frame ownerFrame) {
+  PostCompGui(CharField charField, EditManager eManager, SelectionManager selManager,
+              Frame ownerFrame, int minCompChars) {
     this.charField = charField;
     this.editManager = eManager;
     this.selectionManager = selManager;
     this.owner = ownerFrame;
+    this.minCompChars = minCompChars;
     init();
   }
 
 
-  /** RelDiffGui INNER CLASS */
-  private class RelDiffGui {
-    private CharFieldGui relField;
-    // with embedded/recurse this will be a TermGui...
-    private CharFieldGui diffField;
-    private RelDiffGui() {
-      CharField relChar = new CharField(CharFieldEnum.RELATIONSHIP);
-      Ontology o = charField.getPostCompRelOntol();
-      relChar.addOntology(o);
-      relField = CharFieldGui.makeRelationList(relChar);//"Relationship"?
-      relField.setEditManager(PostCompGui.this.editManager);
-      relField.setSelectionManager(PostCompGui.this.selectionManager);
-      compFieldPanel.addCharFieldGuiToPanel(relField);
-      diffField = CharFieldGui.makePostCompTermList(charField,"Differentia");
-      diffField.setEditManager(PostCompGui.this.editManager);
-      diffField.setSelectionManager(PostCompGui.this.selectionManager);
-      compFieldPanel.addCharFieldGuiToPanel(diffField);
-    }
-    private void setRelDiffModel(RelDiffModel rd) {
-//       try { rd.relField.setRel(getRel(currentTerm)); } catch (Exception e){}
-      relField.setRel(rd.rel);
-      diffField.setOboClass(rd.diff);
-      diffField.setOntologyChooserFromTerm(rd.diff);
-    }
-  } // end of RelDiffGui INNER CLASS
 
-
-  private class RelDiffModel {
-    private OBOProperty rel;
-    private OBOClass diff;
-    private RelDiffModel(OBORestriction link) {
-      rel = link.getType();
-      diff = (OBOClass)link.getParent();
-    }
-  }
-
-
   private void init() {
     // dialog wont be focusable if owner is not showing or something like that
    
@@ -114,6 +82,7 @@
     
     // MAIN GENUS TERM
     genusField = CharFieldGui.makePostCompTermList(charField,"Genus");
+    genusField.setMinCompChars(minCompChars);
     genusField.setSelectionManager(this.selectionManager);
     compFieldPanel.addCharFieldGuiToPanel(genusField);
 
@@ -147,6 +116,44 @@
     dialog.pack();
   }
 
+  /** RelDiffGui INNER CLASS */
+  private class RelDiffGui {
+    private CharFieldGui relField;
+    // with embedded/recurse this will be a TermGui...
+    private CharFieldGui diffField;
+    private RelDiffGui() {
+      CharField relChar = new CharField(CharFieldEnum.RELATIONSHIP);
+      Ontology o = charField.getPostCompRelOntol();
+      relChar.addOntology(o);
+      relField = CharFieldGui.makeRelationList(relChar);//"Relationship"?
+      relField.setMinCompChars(minCompChars);
+      relField.setEditManager(PostCompGui.this.editManager);
+      relField.setSelectionManager(PostCompGui.this.selectionManager);
+      compFieldPanel.addCharFieldGuiToPanel(relField);
+      diffField = CharFieldGui.makePostCompTermList(charField,"Differentia");
+      diffField.setEditManager(PostCompGui.this.editManager);
+      diffField.setSelectionManager(PostCompGui.this.selectionManager);
+      compFieldPanel.addCharFieldGuiToPanel(diffField);
+    }
+    private void setRelDiffModel(RelDiffModel rd) {
+//       try { rd.relField.setRel(getRel(currentTerm)); } catch (Exception e){}
+      relField.setRel(rd.rel);
+      diffField.setOboClass(rd.diff);
+      diffField.setOntologyChooserFromTerm(rd.diff);
+    }
+  } // end of RelDiffGui INNER CLASS
+
+
+  private class RelDiffModel {
+    private OBOProperty rel;
+    private OBOClass diff;
+    private RelDiffModel(OBORestriction link) {
+      rel = link.getType();
+      diff = (OBOClass)link.getParent();
+    }
+  }
+
+
   private void setGuiFromSelectedModel() {
     OBOClass currentTerm = getModelTerm();
     if (currentTerm == null) return;

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-08-28 19:22:41 UTC (rev 835)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-08-28 19:36:48 UTC (rev 836)
@@ -346,7 +346,8 @@
   private class PostCompListener implements ActionListener {
     public void actionPerformed(ActionEvent e) {
       final Frame frame = (Frame)(TermCompList.this.postCompButton.getTopLevelAncestor());
-      new PostCompGui(getCharField(), TermCompList.this.getEditManager(), TermCompList.this.getSelectionManager(), frame);
+      new PostCompGui(getCharField(), TermCompList.this.getEditManager(),
+                      TermCompList.this.getSelectionManager(),frame,getMinCompChars());
     }
   }
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [835] phenote/trunk/conf

From: <nl...@us...> - 2007-08-28 19:22:52

Revision: 835
          http://obo.svn.sourceforge.net/obo/?rev=835&view=rev
Author:   nlw
Date:     2007-08-28 12:22:41 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
renamed the plant config per chih-wei's request

Added Paths:
-----------
    phenote/trunk/conf/plant.cfg

Removed Paths:
-------------
    phenote/trunk/conf/plant_gramene.cfg

Copied: phenote/trunk/conf/plant.cfg (from rev 815, phenote/trunk/conf/plant_gramene.cfg)
===================================================================
--- phenote/trunk/conf/plant.cfg	                        (rev 0)
+++ phenote/trunk/conf/plant.cfg	2007-08-28 19:22:41 UTC (rev 835)
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- *********************** CONFIG INFO ************************** -->
+<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml"
+			  author="Chih-Wei Tung"
+			  description="This configuration is for the plant community.">
+
+  <!-- *********************** SETTINGS **************************** -->
+  <ns:log config-file="conf/log4j-standalone.xml"/>
+  <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/plant_gramene.cfg" />
+
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+
+  <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
+  <ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
+
+  <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
+  <!-- ********************* FILE ADAPTERS ************************** -->
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+
+
+  <!-- ******************** FIELD DEFINITIONS *********************** --> 
+  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
+  <ns:field name="Species" syntax-abbrev="SPECIES" enable="true"/>
+  <ns:field name="Gene" syntax-abbrev="GENE" enable="true"/>
+  <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
+    <ns:ontology name="Genetic Context" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/context.obo"/>
+  </ns:field>
+  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
+    <ns:ontology name="PSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/plant/po_anatomy.obo" />
+    <ns:ontology name="PGSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/plant/po_temporal.obo" />
+    <ns:ontology name="GRO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/cereals/cereals_development.obo" />
+    <ns:ontology name="TO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo" />
+    <ns:ontology name="EO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
+    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
+    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+  </ns:field>
+
+  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
+    <ns:ontology name="PSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/plant/po_anatomy.obo" />
+    <ns:ontology name="PGSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/plant/po_temporal.obo" />
+    <ns:ontology name="GRO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/cereals/cereals_development.obo" />
+    <ns:ontology name="TO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo" />
+    <ns:ontology name="EO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
+    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
+    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+  </ns:field>
+
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+    <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
+  </ns:field>
+
+  <ns:field name="Time" syntax-abbrev="T" enable="true"/>
+  <ns:field name="Count" syntax-abbrev="C" enable="true"/>
+  <ns:field name="Unit" syntax-abbrev="U" enable="true">
+    <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
+  </ns:field>
+  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
+    <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
+  </ns:field>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
+    <ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo" />
+  </ns:field>
+<!-- 06.08.2007 - changed format for files to include url in filename;  added obo repository urls
+     changed gene_ontology to gene_ontology_edit.obo
+     change relationship to ro.obo
+     added auto-update flag
+     added autocomplete setting defaults
+-->
+</ns:phenote-configuration>
\ No newline at end of file

Deleted: phenote/trunk/conf/plant_gramene.cfg
===================================================================
--- phenote/trunk/conf/plant_gramene.cfg	2007-08-28 19:17:27 UTC (rev 834)
+++ phenote/trunk/conf/plant_gramene.cfg	2007-08-28 19:22:41 UTC (rev 835)
@@ -1,82 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- *********************** CONFIG INFO ************************** -->
-<ns:phenote-configuration version="1.3.1" xmlns:ns="phenote/config/xml"
-			  author="Chih-Wei Tung"
-			  description="This configuration is for the plant community.">
-
-  <!-- *********************** SETTINGS **************************** -->
-  <ns:log config-file="conf/log4j-standalone.xml"/>
-  <ns:master-to-local-config mode="UPDATE" when="ON_VERSION_CHANGE" 
-     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/plant_gramene.cfg" />
-
-  <ns:uvic-graph enable="false"/>
-  <ns:term-history enable="false"/>
-
-  <ns:auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
-  <ns:update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds-->
-
-  <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
-
-  <!-- ********************* FILE ADAPTERS ************************** -->
-  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
-  <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
-  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
-
-
-  <!-- ******************** FIELD DEFINITIONS *********************** --> 
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true"/>
-  <ns:field name="Species" syntax-abbrev="SPECIES" enable="true"/>
-  <ns:field name="Gene" syntax-abbrev="GENE" enable="true"/>
-  <ns:field name="Genetic Context" syntax-abbrev="GC" enable="true">
-    <ns:ontology name="Genetic Context" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/context.obo"/>
-  </ns:field>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
-    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
-    <ns:ontology name="PSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/plant/po_anatomy.obo" />
-    <ns:ontology name="PGSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/plant/po_temporal.obo" />
-    <ns:ontology name="GRO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/cereals/cereals_development.obo" />
-    <ns:ontology name="TO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo" />
-    <ns:ontology name="EO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo"/>
-    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
-    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
-    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
-    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
-  </ns:field>
-
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
-    <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
-    <ns:ontology name="PSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/plant/po_anatomy.obo" />
-    <ns:ontology name="PGSO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/plant/po_temporal.obo" />
-    <ns:ontology name="GRO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/developmental/plant_development/cereals/cereals_development.obo" />
-    <ns:ontology name="TO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/plant_traits/plant_trait.obo" />
-    <ns:ontology name="EO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/environment/environment_ontology.obo"/>
-    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo" />
-    <ns:ontology name="CL" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo"/>
-    <ns:ontology name="SO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo"/>
-    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
-  </ns:field>
-
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
-    <ns:ontology name="PATO" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo" />
-  </ns:field>
-
-  <ns:field name="Time" syntax-abbrev="T" enable="true"/>
-  <ns:field name="Count" syntax-abbrev="C" enable="true"/>
-  <ns:field name="Unit" syntax-abbrev="U" enable="true">
-    <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
-  </ns:field>
-  <ns:field name="Abnormal" syntax-abbrev="Tag" enable="true">
-    <ns:ontology name="Abnormal" file="quality.obo" slim="abnormal_slim"/>
-  </ns:field>
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
-  <ns:field name="Evidence" syntax-abbrev="EC" enable="false">
-    <ns:ontology name="Evidence" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo" />
-  </ns:field>
-<!-- 06.08.2007 - changed format for files to include url in filename;  added obo repository urls
-     changed gene_ontology to gene_ontology_edit.obo
-     change relationship to ro.obo
-     added auto-update flag
-     added autocomplete setting defaults
--->
-</ns:phenote-configuration>
\ No newline at end of file


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [834] phenote/trunk/conf/birn2.cfg

From: <mg...@us...> - 2007-08-28 19:17:26

Revision: 834
          http://obo.svn.sourceforge.net/obo/?rev=834&view=rev
Author:   mgibson
Date:     2007-08-28 12:17:27 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
i think birn2 now may be supplanted by birn.cfg - but if it is still used
i think for now we wanna take out config wipeout as birn is starting to mutz 
with configgin

Modified Paths:
--------------
    phenote/trunk/conf/birn2.cfg

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-08-28 19:12:04 UTC (rev 833)
+++ phenote/trunk/conf/birn2.cfg	2007-08-28 19:17:27 UTC (rev 834)
@@ -7,8 +7,8 @@
 
   <!-- wipeout always means that the master will always wipeout the local copy
     in this mode modifying the local is useless -->
-  <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
-     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" />
+  <!-- ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn2.cfg" / -->
 
   <!-- ********************* FILE ADAPTERS ************************** -->
   <!-- be sure to include at least one enabled file adapter -->                                      


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [833] phenote/trunk/conf

From: <mg...@us...> - 2007-08-28 19:12:07

Revision: 833
          http://obo.svn.sourceforge.net/obo/?rev=833&view=rev
Author:   mgibson
Date:     2007-08-28 12:12:04 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
syntax-abbrev is pase - datatag is hip

Modified Paths:
--------------
    phenote/trunk/conf/birn.cfg
    phenote/trunk/conf/birn2.cfg

Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg	2007-08-28 19:05:58 UTC (rev 832)
+++ phenote/trunk/conf/birn.cfg	2007-08-28 19:12:04 UTC (rev 833)
@@ -12,7 +12,7 @@
   <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
   <!--******************** FIELD DEFINITIONS ***********************-->
   <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data" colwidth="150"/>
+  <ns:field name="Pub" datatag="PUB" enable="true" desc="The provenance for this data" colwidth="150"/>
 
 
   <!-- for smart atlas -->
@@ -26,10 +26,10 @@
   <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
   <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
 
-  <ns:field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor" colwidth="67"/>
+  <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor" colwidth="67"/>
   <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely" colwidth="96"/>
 
-  <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="4" enable="true" colwidth="150">
+  <ns:field name="Entity" datatag="E" min-completion-chars="4" enable="true" colwidth="150">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
@@ -43,11 +43,11 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
   </ns:field>
 
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150">
+  <ns:field name="Quality" datatag="Q" enable="true" colwidth="150">
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo" name="Quality"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" min-completion-chars="4" enable="true" colwidth="114">
+  <ns:field name="Add'l Entity" datatag="E2" min-completion-chars="4" enable="true" colwidth="114">
     <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
     <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
@@ -61,9 +61,9 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
   </ns:field>
 
-  <ns:field name="Compare To" syntax-abbrev="Compar" enable="true" colwidth="112"/>
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true" colwidth="189"/>
-  <ns:field name="Comment" syntax-abbrev="Comm" enable="true" colwidth="886"/>
+  <ns:field name="Compare To" datatag="Compar" enable="true" colwidth="112"/>
+  <ns:field name="Description" datatag="Desc" enable="true" colwidth="189"/>
+  <ns:field name="Comment" datatag="Comm" enable="true" colwidth="886"/>
   <!--*********************** SETTINGS ****************************-->
   <ns:uvic-graph enable="false"/>
   <ns:term-history enable="false"/>

Modified: phenote/trunk/conf/birn2.cfg
===================================================================
--- phenote/trunk/conf/birn2.cfg	2007-08-28 19:05:58 UTC (rev 832)
+++ phenote/trunk/conf/birn2.cfg	2007-08-28 19:12:04 UTC (rev 833)
@@ -18,12 +18,12 @@
 
 
   <!-- ******************** FIELD DEFINITIONS *********************** --> 
-  <ns:field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data"/>
+  <ns:field name="Pub" datatag="PUB" enable="true" desc="The provenance for this data"/>
   <ns:field name="Image" enable="true" desc="An image ID for reference"/>
-  <ns:field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a
+  <ns:field name="Organism" enable="true" datatag="GT" desc="This is like the genotype; its probably a
     mouse strain or some other identifying factor"/>
   <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely"/>
-  <ns:field name="Entity" syntax-abbrev="E" enable="true">
+  <ns:field name="Entity" datatag="E" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <ns:ontology name="SAO" file="SAO.obo"/>
@@ -39,11 +39,11 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/ -->
   </ns:field>
 
-  <ns:field name="Quality" syntax-abbrev="Q" enable="true">
+  <ns:field name="Quality" datatag="Q" enable="true">
     <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" syntax-abbrev="E2" enable="true">
+  <ns:field name="Add'l Entity" datatag="E2" enable="true">
      <ns:ontology name="Relationship" is-postcomp-rel="true"
       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
     <!--ns:ontology name="SAO" file="SAO.obo"/-->
@@ -59,9 +59,9 @@
        file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/ -->
   </ns:field>
 
-  <ns:field name="Compare To" syntax-abbrev="Compar" enable="true"/>
+  <ns:field name="Compare To" datatag="Compar" enable="true"/>
 
-  <ns:field name="Description" syntax-abbrev="Desc" enable="true"/>
+  <ns:field name="Description" datatag="Desc" enable="true"/>
 
 
   <!-- *********************** SETTINGS **************************** -->


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [832] phenote/trunk

From: <mg...@us...> - 2007-08-28 19:05:59

Revision: 832
          http://obo.svn.sourceforge.net/obo/?rev=832&view=rev
Author:   mgibson
Date:     2007-08-28 12:05:58 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
can now configure minimum # of characters one has to type in to get completion
hopefully this will help speed up term completion a bit for fields like
entity that have a zillion humoungous ontologies in them and with search all
it starts to crawl
its unclear what a good number to set it to is
with the tradeoff being getting the terms or slowing down
ya should be able to hit down arrow (key or gui) and override this setting
doesnt do this yet
also some other optimizations that could be employed is like obo edit wait
and see whats typed in .1 sec - and cancel previous completions til .1 sec hit
also anytime a new completion comes in the old completion should be cancelled
that will take some tinkering with threading

for birn.cfg entity i set the chars to 4 - we may wanna tinker with that
i think only the entity field it really matters
not going into post comp yet - should

Modified Paths:
--------------
    phenote/trunk/conf/birn.cfg
    phenote/trunk/conf/phenote-config.rnc
    phenote/trunk/conf/phenote-config.xsd
    phenote/trunk/jars/phenoteconfigbeans.jar
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/config/FieldConfig.java
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
    phenote/trunk/src/java/phenote/gui/field/FieldPanel.java

Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/conf/birn.cfg	2007-08-28 19:05:58 UTC (rev 832)
@@ -1,61 +1,80 @@
-<phenote-configuration xmlns="phenote/config/xml">
-                                       
-  <!-- wipeout always means that the master will always wipeout the local copy
-    in this mode modifying the local is useless -->
-  <master-to-local-config mode="WIPEOUT" when="ALWAYS" 
-     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn.cfg" />
+<?xml version="1.0" encoding="UTF-8"?>
+<ns:phenote-configuration version="1.4-beta2" name="BIRN Test Config 2" author="Nicole Washington" description="A test for finding a config for BIRN so I can test annotate from their spreadsheet.  It includes their converted brain subcellular anatomy ontology (SAO)." xmlns:ns="phenote/config/xml">
+  <ns:log config-file="conf/log4j-standalone.xml"/>
+  <!--wipeout always means that the master will always wipeout the local copy
+    in this mode modifying the local is useless-->
+  <!--ns:master-to-local-config mode="WIPEOUT" when="ALWAYS" 
+     overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/birn.cfg" /-->
+  <!--********************* FILE ADAPTERS **************************-->
+  <!--be sure to include at least one enabled file adapter-->
+  <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+  <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
+  <!--******************** FIELD DEFINITIONS ***********************-->
+  <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+  <ns:field name="Pub" syntax-abbrev="PUB" enable="true" desc="The provenance for this data" colwidth="150"/>
 
-  <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
-  <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
-  <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
-  <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/>
 
-  <uvic-graph enable="false"/>
-  <term-history enable="false"/>
+  <!-- for smart atlas -->
+  <ns:field name="Image Name" datatag="imagename" enable="true" desc="Name of image"/>
+  <ns:field name="Image Source" datatag="imagesource" enable="true" desc="Source of image"/>
+  <ns:field name="Annot type" datatag="annotationtype" enable="true" desc="Point,line,area,entireimage"/>
+  <ns:field name="Regions" datatag="regions" enable="true" desc="comma delim list of regions, break into sep chars?"/>
+  <ns:field name="Coordinates" datatag="coordinates" enable="true" desc="coordinates of user selection of image"/>
+  <ns:field name="User Name" datatag="userName" enable="true" desc="should this be hidden?, read only"/>
+  <ns:field name="Timestamp" datatag="timestamp" enable="true" desc="read only, hidden?"/>
+  <ns:field name="Slice Type" datatag="slicetype" enable="true" desc="coronal or sagittal, read only?"/>
+  <ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
 
-  <auto-update-ontologies enable="true"/>  <!--true=update; false=don't update-->
-  <!--set to 0 if you want to bypass the check; time in seconds-->
-  <update-timer timer="10"/>
+  <ns:field name="Organism" enable="true" syntax-abbrev="GT" desc="This is like the genotype; its probably a     mouse strain or some other identifying factor" colwidth="67"/>
+  <ns:field name="Phenotypic Character" enable="true" desc="This is a free-text field for phenotype characters for now, not exactly sure what this captures; it might be just a grouping or it might be conclusions, or something else entirely" colwidth="96"/>
 
-  <field name="Pub" syntax-abbrev="PUB" enable="true"/>
-  <field name="Image" enable="true"/>
-  <field name="Database ID" enable="true"/>
+  <ns:field name="Entity" syntax-abbrev="E" min-completion-chars="4" enable="true" colwidth="150">
+    <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
+    <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
+    <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
+    <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
+    <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
+    <ns:ontology name="CL" file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo"/>
+    <ns:ontology name="Spatial" file="spatial.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+    <!--ns:ontology name="DO" 
+       file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
+  </ns:field>
 
-  <field name="Population" enable="true"/>
-  <field name="Organism" enable="true"/>
-  <field name="Assay" enable="true"/>
+  <ns:field name="Quality" syntax-abbrev="Q" enable="true" colwidth="150">
+    <ns:ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo" name="Quality"/>
+  </ns:field>
 
-  <field name="Entity1" syntax-abbrev="E1" enable="true">
-     <ontology name="Relationship" is-postcomp-rel="true"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo"/>
-    <ontology name="SAO" file="SAO.obo"/>
-    <ontology name="GO"
-       file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
-    <ontology name="CL"
-        file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
-  </field>
+  <ns:field name="Add'l Entity" syntax-abbrev="E2" min-completion-chars="4" enable="true" colwidth="114">
+    <ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
+    <ns:ontology name="SAO" file="SAO_1_2_5.obo"/>
+    <ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
+    <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
+    <ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
+    <ns:ontology name="GO" file="ftp://ftp.geneontology.org/pub/go/ontology/gene_ontology_edit.obo"/>
+    <ns:ontology name="CL" file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo"/>
+    <ns:ontology name="Spatial" file="spatial.obo"/>
+    <ns:ontology name="CHEBI" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+    <!--ns:ontology name="DO" 
+       file="http://www.berkeleybop.org/ontologies/obo-all/disease_ontology/disease_ontology.obo"/-->
+  </ns:field>
 
-  <field name="Type? (eg Tissue)" enable="true"/>
+  <ns:field name="Compare To" syntax-abbrev="Compar" enable="true" colwidth="112"/>
+  <ns:field name="Description" syntax-abbrev="Desc" enable="true" colwidth="189"/>
+  <ns:field name="Comment" syntax-abbrev="Comm" enable="true" colwidth="886"/>
+  <!--*********************** SETTINGS ****************************-->
+  <ns:uvic-graph enable="false"/>
+  <ns:term-history enable="false"/>
+  <ns:auto-update-ontologies enable="true"/>
+  <!--true=update; false=don't update-->
+  <!--set to 0 if you want to bypass the check; time in seconds-->
+  <ns:update-timer timer="10"/>
+  <!--******************** REVISION HISTORY ***********************-->
+  <!--08.14.2007 - Sarah M. copied from birn2
+      - added comment field
+      - added link to FMA repository ontology page-->
+  <ns:data-input-servlet/>
+</ns:phenote-configuration>
 
-  <field name="Quality" syntax-abbrev="Q" enable="true">
-    <ontology file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/>
-  </field>
-
-  <field name="Entity2" syntax-abbrev="E2" enable="true">
-     <ontology name="Relationship" is-postcomp-rel="true"
-      file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo"/>
-    <ontology name="SAO" file="SAO.obo"/>
-    <ontology name="GO"
-     file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
-    <ontology name="CL"
-        file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
-  </field>
-
-  <field name="Evidence" syntax-abbrev="EC" enable="true">
-    <ontology name="Evidence"
-     file="http://www.berkeleybop.org/ontologies/obo-all/evidence_code/evidence_code.obo"/>
-  </field>
-
-  <field name="Compare To" enable="true"/>
-
-</phenote-configuration>

Modified: phenote/trunk/conf/phenote-config.rnc
===================================================================
--- phenote/trunk/conf/phenote-config.rnc	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/conf/phenote-config.rnc	2007-08-28 19:05:58 UTC (rev 832)
@@ -101,6 +101,9 @@
     ## whether to copy the field when character is copied/duplicated
     ## a database id usually shouldnt be copied, default true
     attribute copy-field { xsd:boolean },
+    ## the amount of letters/chars a user has to type before completion happens
+    ## this is to optimize slow completion w many ontologies 
+    attribute min-completion-chars { xsd:int },
     postcomp?,
     ontology*
   } 

Modified: phenote/trunk/conf/phenote-config.xsd
===================================================================
--- phenote/trunk/conf/phenote-config.xsd	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/conf/phenote-config.xsd	2007-08-28 19:05:58 UTC (rev 832)
@@ -119,6 +119,7 @@
       <xs:attribute name="repos-subdir" use="required" type="xs:string"/>
       <xs:attribute name="groups" type="xs:IDREFS"/>
       <xs:attribute name="copy-field" use="required" type="xs:boolean"/>
+      <xs:attribute name="min-completion-chars" use="required" type="xs:int"/>
     </xs:complexType>
   </xs:element>
   <xs:element name="ontology">

Modified: phenote/trunk/jars/phenoteconfigbeans.jar
===================================================================
(Binary files differ)

Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/src/java/phenote/config/Config.java	2007-08-28 19:05:58 UTC (rev 832)
@@ -727,6 +727,14 @@
   	getEnbldFieldCfg(index).setColwidth(width);
   }
 
+  public int getMinCompChars(int fieldIndex) {
+    if (!hasEnbldCharField(fieldIndex)) {
+      log().error("No char field for index "+fieldIndex);
+      return 0; // throw ex?
+    }
+    return getEnbldFieldCfg(fieldIndex).getMinCompletionChars();
+  }
+
 //   public CharFieldEnum getCharFieldEnum(int index) {
 //     return getFieldConfig(index).getCharFieldEnum();
 //   }

Modified: phenote/trunk/src/java/phenote/config/FieldConfig.java
===================================================================
--- phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/src/java/phenote/config/FieldConfig.java	2007-08-28 19:05:58 UTC (rev 832)
@@ -133,6 +133,14 @@
   	fieldBean.setColwidth(w);
   	return;
   }
+
+  /** Return the amount of letters/chars a user has to type before completion
+      kicks in - this helps with slow completion with many ontologies on a slow
+      computer */
+  public int getMinCompletionChars() {
+    // i think if unconfigged/uninitialized defaults to 0 which is what we want
+    return fieldBean.getMinCompletionChars();
+  }
   
   // boolean hasLabel(String label) { return label.equals(this.label); } 
   boolean hasDesc(String desc) { return desc.equals(this.desc); }

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-08-28 19:05:58 UTC (rev 832)
@@ -44,6 +44,8 @@
   private SearchParamsI searchParams = SearchParams.inst();
   private CompListSearcher compListSearcher;
   private boolean setGuiForMultiSelect = false;
+  // minimum chars to type for completion to happen - from config
+  private int minCompChars = 0;
 
   protected AbstractAutoCompList(CharField cf) {
     super(cf);
@@ -61,6 +63,8 @@
     doCompletion(false); // dont show popup - we dont have a gui yet, just populating
   }
 
+  public void setMinCompChars(int minChars) { minCompChars = minChars; }
+
   protected Component getUserInputGui() { return jComboBox; }
 
   protected boolean isCompList() { return true; }
@@ -239,6 +243,8 @@
     
     // too soon - text field doesnt have text yet.... hmmmm....
     String input = getText();
+    // If length of input is shorter than minimum required for completion do nothing
+    if (input.length() < minCompChars) return;
     // returns a list of CompletionTerms (checks if relations)
     // if input is empty will return whole list (if configged)
     //log().debug("got new completion request for input "+input+" time "+time());

Modified: phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/src/java/phenote/gui/field/CharFieldGui.java	2007-08-28 19:05:58 UTC (rev 832)
@@ -523,6 +523,9 @@
   // for subclasses to override
   protected void returnKeyHit() {}
 
+  /** no op - override in term completion gui */
+  public void setMinCompChars(int minCompChars) {}
+
   private Logger log;
   private Logger log() {
     if (log == null) log = Logger.getLogger(getClass());

Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-08-28 18:53:20 UTC (rev 831)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java	2007-08-28 19:05:58 UTC (rev 832)
@@ -133,9 +133,12 @@
         fieldPanel = new JPanel(new GridBagLayout());
         jTabbedPane.addTab("Tab "+tab++,fieldPanel);
       }
+      CharFieldGui gui = CharFieldGui.makeCharFieldGui(charField);
+      if (charField.isTerm()) {
+        int minCompChars = Config.inst().getMinCompChars(fieldNum);
+        gui.setMinCompChars(minCompChars);
+      }
       ++fieldNum;
-      //CharFieldGui gui = new CharFieldGui(charField,this); // adds to panel
-      CharFieldGui gui = CharFieldGui.makeCharFieldGui(charField);
       gui.setSelectionManager(this.selectionManager);
       gui.setEditManager(this.editManager);
       addCharFieldGuiToPanel(gui);


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [831] phenote/trunk

From: <ba...@us...> - 2007-08-28 18:53:18

Revision: 831
          http://obo.svn.sourceforge.net/obo/?rev=831&view=rev
Author:   balhoff
Date:     2007-08-28 11:53:20 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
Added ability to mark all selected character templates.

Modified Paths:
--------------
    phenote/trunk/conf/character_template.xml
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
    phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java

Modified: phenote/trunk/conf/character_template.xml
===================================================================
--- phenote/trunk/conf/character_template.xml	2007-08-28 17:28:19 UTC (rev 830)
+++ phenote/trunk/conf/character_template.xml	2007-08-28 18:53:20 UTC (rev 831)
@@ -17,6 +17,7 @@
 	        <button id="duplicateButton" text="Duplicate" action="duplicateSelectedCharacters"/>
 	        <button id="deleteButton" text="Delete" action="deleteSelectedCharacters"/>
 	        <button id="undoButton" text="Undo" action="undo"/>
+	        <button id="markButton" text="Mark Selected" action="markSelectedCharacters"/>
 	        <button id="invertSelectionButton" text="Invert Marked" action="invertMarkedCharacters"/>
 	        <button id="generateButton" text="Generate Characters" action="generateCharacters"/>
 	    </panel>

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-28 17:28:19 UTC (rev 830)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java	2007-08-28 18:53:20 UTC (rev 831)
@@ -101,6 +101,10 @@
     this.editManager.copyChars(this.selectionManager.getSelectedChars());
   }
   
+  public void markSelectedCharacters() {
+    this.tableModel.markCharactersInRows(this.characterTemplateTable.getSelectedRows());
+  }
+  
   public void undo() {
     this.editManager.undo();
   }

Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-28 17:28:19 UTC (rev 830)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateTableModel.java	2007-08-28 18:53:20 UTC (rev 831)
@@ -76,6 +76,12 @@
       this.setCharacterIsMarked(character, !this.isCharacterMarked(character));
     }
   }
+  
+  public void markCharactersInRows(int[] rows) {
+    for (int row : rows) {
+      this.setCharacterIsMarked(this.getCharacterAtRow(row), true);
+    }
+  }
 
   public int getColumnCount() {
     return Config.inst().getFieldsInGroup(this.representedGroup).size() + 1;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [830] phenote/trunk/src/java/phenote/main/PhenoteVersion. java

From: <mg...@us...> - 2007-08-28 17:28:17

Revision: 830
          http://obo.svn.sourceforge.net/obo/?rev=830&view=rev
Author:   mgibson
Date:     2007-08-28 10:28:19 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
woops

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-08-28 17:27:16 UTC (rev 829)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-08-28 17:28:19 UTC (rev 830)
@@ -9,7 +9,7 @@
 
 public class PhenoteVersion {
 
-  private String hardwiredDefaultVersion = "1.4-beta3";
+  private static String hardwiredDefaultVersion = "1.4-beta3";
 
   public static String versionString() {
     final String version = System.getProperty("phenote.version");


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Obo-svn-commit] SF.net SVN: obo: [829] phenote/trunk/src/java/phenote/main/PhenoteVersion. java

From: <mg...@us...> - 2007-08-28 17:27:14

Revision: 829
          http://obo.svn.sourceforge.net/obo/?rev=829&view=rev
Author:   mgibson
Date:     2007-08-28 10:27:16 -0700 (Tue, 28 Aug 2007)

Log Message:
-----------
jim - if you have a better way than this hardwire that doesnt rely on property
go ahead and ammend this - just putting back hardwired version for now for
this release 

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/main/PhenoteVersion.java

Modified: phenote/trunk/src/java/phenote/main/PhenoteVersion.java
===================================================================
--- phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-08-28 17:01:10 UTC (rev 828)
+++ phenote/trunk/src/java/phenote/main/PhenoteVersion.java	2007-08-28 17:27:16 UTC (rev 829)
@@ -9,13 +9,16 @@
 
 public class PhenoteVersion {
 
+  private String hardwiredDefaultVersion = "1.4-beta3";
+
   public static String versionString() {
     final String version = System.getProperty("phenote.version");
     if (version != null) {
       return version;
     } else {
-      log().error("Version information not found");
-      return "";
+      log().info("Version information not found as property, going with hardwired default of "+hardwiredDefaultVersion);
+      
+      return hardwiredDefaultVersion;
     }
   }
   


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

363 messages has been excluded from this view by a project administrator.

Flat | Threaded

<< < 1 .. 151 152 153 154 155 .. 183 > >> (Page 153 of 183)